Variant report

Variant	rs6546862
Chromosome Location	chr2:73860348-73860349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10190002	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap]
rs1052161	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs10865398	0.96[CEU][hapmap];0.82[GIH][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs11126407	0.97[ASN][1000 genomes]
rs11126408	0.97[ASN][1000 genomes]
rs11126409	0.97[ASN][1000 genomes]
rs11126411	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11126413	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11126414	0.81[TSI][hapmap]
rs11126415	0.80[EUR][1000 genomes]
rs11126417	0.81[TSI][hapmap]
rs11680056	0.91[ASN][1000 genomes]
rs11689234	0.82[CHB][hapmap]
rs11894953	0.81[TSI][hapmap]
rs12052539	0.80[EUR][1000 genomes]
rs12053242	0.80[EUR][1000 genomes]
rs12151671	0.97[ASN][1000 genomes]
rs12478871	0.91[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs12618600	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs12620018	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12620091	0.80[CEU][hapmap];0.82[AFR][1000 genomes]
rs12620569	0.97[ASN][1000 genomes]
rs12713793	0.81[TSI][hapmap]
rs12713798	0.81[TSI][hapmap]
rs12991161	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13007607	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13007623	0.97[ASN][1000 genomes]
rs13017182	1.00[CEU][hapmap];0.84[GIH][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs13018422	0.94[EUR][1000 genomes]
rs13022145	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027816	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320374	1.00[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17350125	0.80[EUR][1000 genomes]
rs17350188	0.81[TSI][hapmap]
rs1879662	0.96[ASN][1000 genomes]
rs1879666	0.97[ASN][1000 genomes]
rs2280506	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2280507	0.93[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2421574	0.92[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2421582	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2421583	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2421584	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421586	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2421587	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2421589	0.95[ASN][1000 genomes]
rs2421590	0.97[ASN][1000 genomes]
rs2421591	0.95[ASN][1000 genomes]
rs2421667	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2421668	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap]
rs2421674	0.81[TSI][hapmap]
rs2421676	0.81[TSI][hapmap]
rs28708576	0.96[ASN][1000 genomes]
rs2947845	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs34719281	0.97[ASN][1000 genomes]
rs34874205	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35421685	0.83[EUR][1000 genomes]
rs35498419	0.80[EUR][1000 genomes]
rs3980696	0.91[ASN][1000 genomes]
rs4341964	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346412	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4443018	0.96[ASN][1000 genomes]
rs4444558	0.81[ASN][1000 genomes]
rs4627598	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4852310	0.97[ASN][1000 genomes]
rs4852311	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4852316	0.81[EUR][1000 genomes]
rs4852939	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4852948	0.96[ASN][1000 genomes]
rs4852949	0.97[ASN][1000 genomes]
rs4852950	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4852951	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4852953	0.86[ASN][1000 genomes]
rs4852954	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4852956	0.95[ASN][1000 genomes]
rs4852957	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4852958	0.93[ASN][1000 genomes]
rs4852959	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4852975	0.81[TSI][hapmap]
rs4852976	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs6546863	0.97[ASN][1000 genomes]
rs6718799	0.95[ASN][1000 genomes]
rs6722867	0.82[EUR][1000 genomes]
rs6725284	0.95[ASN][1000 genomes]
rs6729347	0.97[ASN][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6742619	0.91[CEU][hapmap]
rs6743576	0.82[EUR][1000 genomes]
rs6744273	0.87[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6745560	0.96[CEU][hapmap];0.82[GIH][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap]
rs6749680	0.84[CEU][hapmap];0.86[MKK][hapmap]
rs6755948	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7210	0.83[TSI][hapmap]
rs72811975	0.91[ASN][1000 genomes]
rs7558546	0.80[EUR][1000 genomes]
rs7570683	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7574240	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7574268	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7579068	0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7585668	0.97[ASN][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs7599453	0.80[EUR][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7607989	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7609249	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1015036	chr2:73840055-73891004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1006235	chr2:73840055-73896603	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1006033	chr2:73840055-73900856	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2760600	chr2:73846605-73911523	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874271	chr2:73847024-73907696	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv874272	chr2:73847024-73914019	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv874273	chr2:73847024-73916672	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv874274	chr2:73847024-73922475	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv874275	chr2:73847024-73931971	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
18	nsv979021	chr2:73847283-73871861	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1013586	chr2:73848777-73906844	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1004208	chr2:73849172-73911511	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	esv2497164	chr2:73850717-73912022	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1004886	chr2:73852525-73900856	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1011488	chr2:73852525-73909818	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv1000057	chr2:73852525-73911511	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	esv3385057	chr2:73853505-73913858	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1013142	chr2:73854911-73911511	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv1008311	chr2:73854911-73923089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv829460	chr2:73856145-73913711	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv582209	chr2:73857002-73907696	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	nsv818044	chr2:73859184-73906819	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
31	nsv515605	chr2:73859184-73916672	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6546862	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs6546862	ALMS1P	cis	Nerve Tibial	GTEx
rs6546862	ALMS1P	cis	cerebellum	SCAN
rs6546862	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs6546862	DUSP11	cis	cerebellum	SCAN
rs6546862	ALMS1	cis	parietal	SCAN
rs6546862	ALMS1	cis	cerebellum	SCAN
rs6546862	ALMS1P	cis	parietal	SCAN
rs6546862	DUSP11	cis	parietal	SCAN
rs6546862	MPHOSPH10	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73859800-73860400	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links