Variant report

Variant	rs6587628
Chromosome Location	chr1:151850072-151850073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151811092..151813257-chr1:151850027..151851704,2	K562	blood:
2	chr1:151827756..151830746-chr1:151848383..151850324,3	MCF-7	breast:
3	chr1:151849295..151852106-chr1:151882235..151884550,2	K562	blood:
4	chr1:151848144..151850856-chr1:151866244..151868126,2	MCF-7	breast:
5	chr1:151814117..151815880-chr1:151848730..151850966,2	MCF-7	breast:
6	chr1:151843139..151845993-chr1:151848350..151850912,2	K562	blood:

Variant related genes	Relation type
ENSG00000225556	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000234614	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1003107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10158030	1.00[CHB][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1038746	1.00[CHB][hapmap]
rs1038748	1.00[CHB][hapmap]
rs1048910	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10749666	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs10788814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10788816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10888450	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888451	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204905	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11204911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204912	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723616	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1352654	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387834	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs1387835	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs1490187	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs1490190	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1490191	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[ASN][1000 genomes]
rs1552606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1552607	1.00[CHB][hapmap]
rs1602245	1.00[CHB][hapmap]
rs1602248	1.00[CHB][hapmap]
rs17583707	1.00[CHB][hapmap]
rs1844542	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1873310	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1873311	1.00[CHB][hapmap]
rs1873312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1967085	1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2054948	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2087549	0.90[GIH][hapmap];0.90[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2130526	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2171917	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2338018	1.00[CHB][hapmap]
rs2338200	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338203	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2338204	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2338210	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932563	1.00[CHB][hapmap]
rs2932567	1.00[CHB][hapmap]
rs2932578	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2932584	0.88[ASN][1000 genomes]
rs2932592	1.00[CHB][hapmap]
rs2999514	1.00[CHB][hapmap]
rs2999527	1.00[CHB][hapmap]
rs2999529	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs2999535	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs2999538	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs2999551	1.00[CHB][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap]
rs2999558	1.00[CHB][hapmap]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap]
rs3007676	1.00[CHB][hapmap]
rs3007679	1.00[CHB][hapmap]
rs3007682	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3007690	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs3007692	0.88[ASN][1000 genomes]
rs3007700	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs3007701	1.00[CHB][hapmap]
rs3007704	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap]
rs3122300	1.00[CHB][hapmap]
rs3122301	1.00[CHB][hapmap]
rs34370890	0.91[ASN][1000 genomes]
rs3748805	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762427	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4551598	0.92[EUR][1000 genomes]
rs4845385	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845664	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845699	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587626	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587627	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587641	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs6659029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6662463	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6678664	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690443	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6691350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7529451	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7532721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544380	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7545863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552869	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs902314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902316	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959945	1.00[CHB][hapmap];0.90[MEX][hapmap]
rs9943225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription 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	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6587628	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs6587628	S100A10	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151832000-151859600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:151840600-151864600	Weak transcription	NH-A	brain
4	chr1:151840800-151857800	Weak transcription	K562	blood
5	chr1:151841200-151859200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:151841200-151880800	Weak transcription	NHLF	lung
7	chr1:151841400-151860000	Weak transcription	Hela-S3	cervix
8	chr1:151841400-151860200	Weak transcription	Osteobl	bone
9	chr1:151841600-151864000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:151843400-151859600	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:151844000-151860000	Weak transcription	HSMM	muscle
12	chr1:151844000-151864600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:151844200-151859600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:151844200-151860400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr1:151844400-151857800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:151844400-151866400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
18	chr1:151844600-151851600	Weak transcription	Fetal Brain Male	brain
19	chr1:151844600-151853800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:151844600-151863600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:151844600-151864200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:151844800-151853800	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:151844800-151857800	Weak transcription	HMEC	breast
24	chr1:151844800-151863800	Weak transcription	Brain Substantia Nigra	brain
25	chr1:151844800-151864200	Weak transcription	Pancreas	Pancrea
26	chr1:151844800-151870800	Weak transcription	Gastric	stomach
27	chr1:151844800-151871200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:151845200-151863600	Weak transcription	Fetal Kidney	kidney
30	chr1:151845400-151871200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:151845600-151851600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:151845800-151851200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:151845800-151859200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:151846000-151861800	Weak transcription	Psoas Muscle	Psoas
35	chr1:151846000-151864200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:151846200-151851200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:151846200-151858000	Weak transcription	A549	lung
38	chr1:151846400-151855400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:151846400-151859600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:151846400-151860000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr1:151846400-151860200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr1:151846400-151865400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:151846400-151870400	Weak transcription	Right Ventricle	heart
44	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:151846600-151851000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:151846600-151859400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:151846600-151864800	Weak transcription	Fetal Lung	lung
48	chr1:151846800-151858000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:151846800-151860400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:151846800-151860400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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