Variant report

Variant	rs6689417
Chromosome Location	chr1:46388008-46388009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46383655..46385679-chr1:46387567..46389104,2	K562	blood:

Extended variants
information (count: 152 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10736427	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749859	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749861	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789476	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789477	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789482	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890356	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890357	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10890379	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211186	1.00[ASN][1000 genomes]
rs11211206	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211211	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211214	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211220	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11211247	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580953	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582058	0.91[CEU][hapmap]
rs11584814	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587648	1.00[ASN][1000 genomes]
rs11805376	1.00[ASN][1000 genomes]
rs12045409	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047120	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355641	1.00[ASN][1000 genomes]
rs17855317	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067635	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795318	0.85[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256763	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300171	1.00[ASN][1000 genomes]
rs4364819	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382655	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388641	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420029	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs4423055	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4434876	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4474301	1.00[ASN][1000 genomes]
rs4524993	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4557909	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4573476	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660315	1.00[ASN][1000 genomes]
rs4660330	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660333	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660887	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660891	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660893	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660901	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660909	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55641506	1.00[ASN][1000 genomes]
rs55652826	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55735913	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55765474	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047133	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140667	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56278140	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56295206	1.00[ASN][1000 genomes]
rs56301932	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56316933	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56368769	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59091734	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429579	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429590	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429592	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429593	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659064	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662307	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665193	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666501	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669534	1.00[ASN][1000 genomes]
rs6673894	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674105	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680333	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6680647	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685465	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693222	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696284	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs6700322	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700974	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702764	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677518	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677530	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677533	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677541	1.00[ASN][1000 genomes]
rs72677543	1.00[ASN][1000 genomes]
rs72677545	1.00[ASN][1000 genomes]
rs72677546	1.00[ASN][1000 genomes]
rs72677550	1.00[ASN][1000 genomes]
rs72677553	1.00[ASN][1000 genomes]
rs72677556	1.00[ASN][1000 genomes]
rs72677559	1.00[ASN][1000 genomes]
rs72690847	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690855	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72690901	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692603	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692613	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692632	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692639	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413189	0.81[EUR][1000 genomes]
rs7512448	0.89[EUR][1000 genomes]
rs7517418	1.00[ASN][1000 genomes]
rs7525281	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530480	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532388	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533750	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7548617	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552810	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555458	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556472	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884443	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429090	0.95[CEU][hapmap];1.00[ASN][1000 genomes]
rs9429091	0.82[EUR][1000 genomes]
rs9429093	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429179	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429184	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429187	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9429188	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
6	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
9	nsv1000498	chr1:46171836-46438252	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv870791	chr1:46182916-46398415	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1003986	chr1:46184925-46417621	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	nsv1007501	chr1:46184925-46439533	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
13	nsv534944	chr1:46184925-46439533	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv1006891	chr1:46189258-46408032	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv1009355	chr1:46189258-46463012	Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
16	nsv546158	chr1:46216575-46495434	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
17	nsv870911	chr1:46216575-46498375	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
18	nsv431268	chr1:46223080-46495480	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv546159	chr1:46223086-46398415	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv461417	chr1:46223086-46416348	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv546160	chr1:46223086-46416348	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv524147	chr1:46236098-46438076	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv1007162	chr1:46244432-46417621	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv1015136	chr1:46244432-46439533	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
25	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
26	nsv1007759	chr1:46248667-46493959	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
27	nsv534945	chr1:46248667-46493959	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
28	nsv916232	chr1:46248686-46493918	Genic enhancers Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
29	nsv437479	chr1:46272879-46411146	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
30	nsv1009527	chr1:46286329-46520127	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
31	nsv546161	chr1:46311275-46498375	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
32	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
33	nsv1003554	chr1:46331254-46410657	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
34	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
35	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
36	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
37	nsv829737	chr1:46352900-46506424	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
38	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6689417	CCDC163P	cis	Artery Tibial	GTEx
rs6689417	CCDC163P	cis	Esophagus Mucosa	GTEx
rs6689417	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs6689417	CCDC163P	cis	lung	GTEx
rs6689417	CCDC163P	cis	Muscle Skeletal	GTEx
rs6689417	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs6689417	CCDC163P	cis	Artery Aorta	GTEx
rs6689417	CCDC163P	cis	Stomach	GTEx
rs6689417	CCDC163P	cis	Nerve Tibial	GTEx
rs6689417	CCDC163P	cis	Heart Left Ventricle	GTEx
rs6689417	CCDC163P	cis	Thyroid	GTEx
rs6689417	CCDC163P	cis	Esophagus Muscularis	GTEx
rs6689417	CCDC163P	cis	Whole Blood	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46342200-46391200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:46363000-46393800	Weak transcription	A549	lung
3	chr1:46373000-46395000	Weak transcription	Gastric	stomach
4	chr1:46379400-46390200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:46379600-46390000	Weak transcription	GM12878-XiMat	blood
6	chr1:46379600-46394600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:46379800-46389200	Weak transcription	Fetal Brain Male	brain
8	chr1:46379800-46390400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:46379800-46394600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:46379800-46395000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:46379800-46395200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:46380000-46388600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:46380000-46392200	Weak transcription	Fetal Brain Female	brain
14	chr1:46380400-46391800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:46380400-46394800	Weak transcription	NHDF-Ad	bronchial
16	chr1:46380400-46395000	Weak transcription	NHLF	lung
17	chr1:46380600-46394800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:46380800-46391200	Weak transcription	Thymus	Thymus
19	chr1:46380800-46394200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:46380800-46394400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:46380800-46395000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:46380800-46404600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr1:46381000-46388400	Weak transcription	Spleen	Spleen
24	chr1:46381000-46390600	Weak transcription	Small Intestine	intestine
25	chr1:46381000-46391200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:46381000-46391400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:46381600-46388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:46383200-46393600	Weak transcription	Dnd41	blood
29	chr1:46383600-46390600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:46383600-46394200	Weak transcription	HepG2	liver
31	chr1:46384200-46389600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:46384200-46390600	Weak transcription	HSMMtube	muscle
33	chr1:46384600-46388600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:46385600-46389000	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:46385600-46391400	Weak transcription	HSMM	muscle
36	chr1:46386600-46388800	Weak transcription	Primary T cells from cord blood	blood
37	chr1:46386800-46389800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:46387000-46388400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:46387000-46388600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:46387000-46389000	Strong transcription	Fetal Intestine Small	intestine
41	chr1:46387000-46389000	Strong transcription	Fetal Stomach	stomach
42	chr1:46387000-46389000	Enhancers	Left Ventricle	heart
43	chr1:46387000-46389000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
44	chr1:46387000-46389800	Enhancers	Fetal Heart	heart
45	chr1:46387200-46388200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr1:46387200-46388400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:46387200-46388600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
48	chr1:46387200-46389000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:46387400-46389000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:46387600-46388200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links