Variant report

Variant	rs10864004
Chromosome Location	chr1:213009469-213009470
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213000835..213002742-chr1:213006925..213009621,2	K562	blood:

Extended variants
information (count: 177 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1047881	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10746439	0.89[ASN][1000 genomes]
rs10779585	0.95[ASN][1000 genomes]
rs10779586	0.95[ASN][1000 genomes]
rs10779587	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10779588	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs10779589	0.86[ASN][1000 genomes]
rs10779590	0.90[ASN][1000 genomes]
rs10779591	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs10779592	0.90[ASN][1000 genomes]
rs10779595	0.90[ASN][1000 genomes]
rs10864007	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864009	0.95[ASN][1000 genomes]
rs10864010	0.95[ASN][1000 genomes]
rs10864015	0.95[ASN][1000 genomes]
rs10864016	0.90[ASN][1000 genomes]
rs10864018	0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10864020	0.89[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs10864022	0.86[ASN][1000 genomes]
rs10902	0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11120042	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs11120043	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs11120047	0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11120049	0.95[ASN][1000 genomes]
rs11120050	0.90[ASN][1000 genomes]
rs11120053	0.92[ASN][1000 genomes]
rs11120054	0.89[ASN][1000 genomes]
rs11120055	0.88[ASN][1000 genomes]
rs11120056	0.90[ASN][1000 genomes]
rs11120057	0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11120059	0.89[ASN][1000 genomes]
rs11120060	0.90[ASN][1000 genomes]
rs11120064	0.83[ASN][1000 genomes]
rs11803450	0.90[ASN][1000 genomes]
rs11806446	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808574	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12022540	0.97[ASN][1000 genomes]
rs12023052	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs12030572	0.84[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12031546	0.90[ASN][1000 genomes]
rs12036698	0.90[ASN][1000 genomes]
rs12040103	0.90[ASN][1000 genomes]
rs12042181	0.85[CHD][hapmap]
rs12043346	0.95[ASN][1000 genomes]
rs12043852	0.90[ASN][1000 genomes]
rs12048942	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12069595	0.90[ASN][1000 genomes]
rs12118361	0.95[ASN][1000 genomes]
rs12122682	0.90[ASN][1000 genomes]
rs12123978	0.92[ASN][1000 genomes]
rs12125982	1.00[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs12136117	0.84[ASN][1000 genomes]
rs12140831	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs12565125	0.83[ASN][1000 genomes]
rs12566087	0.90[ASN][1000 genomes]
rs12567713	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12567728	0.87[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs12731517	0.90[ASN][1000 genomes]
rs12735221	0.90[ASN][1000 genomes]
rs12744746	0.90[ASN][1000 genomes]
rs12756625	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1284860	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1472342	0.90[ASN][1000 genomes]
rs1587174	0.88[ASN][1000 genomes]
rs17019818	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17019870	0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17019873	0.88[ASN][1000 genomes]
rs1874416	0.95[ASN][1000 genomes]
rs1874417	0.89[ASN][1000 genomes]
rs1874418	0.95[ASN][1000 genomes]
rs1874420	0.89[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1890932	0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2047287	0.89[ASN][1000 genomes]
rs2132431	0.94[ASN][1000 genomes]
rs2172983	0.87[ASN][1000 genomes]
rs2185487	0.87[ASN][1000 genomes]
rs2201602	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2201603	0.94[ASN][1000 genomes]
rs2220949	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2279692	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs2291771	0.90[ASN][1000 genomes]
rs2291772	0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2291773	0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2497959	0.85[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2644548	0.85[ASW][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3768548	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3768550	0.95[ASN][1000 genomes]
rs3768551	0.87[ASN][1000 genomes]
rs41296726	0.90[ASN][1000 genomes]
rs41297446	0.91[ASN][1000 genomes]
rs41300993	0.90[ASN][1000 genomes]
rs41301027	0.88[ASN][1000 genomes]
rs4951465	0.91[ASN][1000 genomes]
rs4951466	0.90[ASN][1000 genomes]
rs4951470	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs4951472	0.87[ASN][1000 genomes]
rs4951644	0.91[ASN][1000 genomes]
rs4951645	0.91[ASN][1000 genomes]
rs4951646	0.90[ASN][1000 genomes]
rs4951647	0.90[ASN][1000 genomes]
rs55793082	0.87[ASN][1000 genomes]
rs56178110	0.90[ASN][1000 genomes]
rs6540769	1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs6657416	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6659996	0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6664909	0.94[ASN][1000 genomes]
rs6666167	0.90[ASN][1000 genomes]
rs6666277	0.91[CHB][hapmap]
rs6666356	0.91[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6666368	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs6685877	0.91[ASN][1000 genomes]
rs6697428	0.95[ASN][1000 genomes]
rs6700342	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6703156	0.92[ASN][1000 genomes]
rs72743967	0.90[ASN][1000 genomes]
rs72743981	0.88[ASN][1000 genomes]
rs72743991	0.84[ASN][1000 genomes]
rs72743993	0.82[ASN][1000 genomes]
rs7512393	0.90[ASN][1000 genomes]
rs7516718	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7516817	0.89[ASN][1000 genomes]
rs7519166	0.90[ASN][1000 genomes]
rs7522693	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7522877	0.90[ASN][1000 genomes]
rs7524203	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528505	1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs7530561	0.88[ASN][1000 genomes]
rs7531073	0.90[ASN][1000 genomes]
rs7534973	0.91[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs7536716	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7538797	0.88[ASN][1000 genomes]
rs7544198	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7544567	0.97[ASN][1000 genomes]
rs7544645	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs963328	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs9787376	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv549149	chr1:212997385-213009657	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
3	nsv508691	chr1:212998319-213028392	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
4	nsv549150	chr1:212999701-213011812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv549154	chr1:213002088-213009469	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv549155	chr1:213002088-213009657	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	esv2421907	chr1:213002088-213010436	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv549156	chr1:213002088-213011812	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv549157	chr1:213002088-213018125	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv8791	chr1:213002097-213014844	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	esv3321128	chr1:213002226-213013781	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv826564	chr1:213002232-213013565	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	esv3321127	chr1:213002235-213013744	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	esv3321126	chr1:213002278-213013753	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
15	esv3321130	chr1:213002280-213013711	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
16	esv3349041	chr1:213002330-213013685	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	esv3321131	chr1:213002369-213013669	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
18	nsv549160	chr1:213003428-213009469	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv549161	chr1:213003428-213009657	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
20	nsv549162	chr1:213003428-213011812	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
21	nsv549163	chr1:213003428-213018125	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
22	esv2763825	chr1:213004455-213014453	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
23	esv10902	chr1:213004863-213013140	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
24	nsv514041	chr1:213004993-213010369	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
25	nsv549166	chr1:213005012-213009469	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
26	nsv549167	chr1:213005012-213009657	Weak transcription Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
27	esv1830149	chr1:213005012-213010436	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
28	nsv549168	chr1:213005012-213011812	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
29	nsv549169	chr1:213005012-213018125	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
30	nsv441735	chr1:213005015-213010436	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
31	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
32	nsv549170	chr1:213005344-213009657	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
33	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
34	nsv549171	chr1:213005877-213009657	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
35	nsv549172	chr1:213005877-213011812	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
36	nsv549173	chr1:213005941-213011812	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
37	nsv549174	chr1:213006058-213009657	Flanking Active TSS Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
38	nsv549175	chr1:213006058-213018125	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
39	esv32562	chr1:213006064-213009497	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
40	nsv549176	chr1:213006397-213009657	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
41	nsv549177	chr1:213007465-213009657	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10864004	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs10864004	FLVCR1-AS1	cis	lung	GTEx
rs10864004	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs10864004	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs10864004	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs10864004	FLVCR1-AS1	cis	Whole Blood	GTEx
rs10864004	LQK1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213005800-213009800	Enhancers	Fetal Intestine Small	intestine
2	chr1:213009400-213009600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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