Variant report

Variant	rs7555292
Chromosome Location	chr1:93789148-93789149
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93788744..93790531-chr1:93809891..93812646,2	MCF-7	breast:
2	chr1:93767244..93769899-chr1:93787489..93789532,2	K562	blood:
3	chr1:93786566..93790038-chr1:93805342..93808544,3	K562	blood:

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1000606	0.97[EUR][1000 genomes]
rs10430073	0.97[EUR][1000 genomes]
rs10782958	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1081523	0.87[EUR][1000 genomes]
rs1081524	0.89[EUR][1000 genomes]
rs1081525	0.90[EUR][1000 genomes]
rs1081526	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10874771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874774	0.92[EUR][1000 genomes]
rs10874775	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1088319	0.89[EUR][1000 genomes]
rs11164878	0.82[EUR][1000 genomes]
rs11164882	0.85[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11164888	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164889	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164890	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164891	0.95[EUR][1000 genomes]
rs11164906	0.97[EUR][1000 genomes]
rs11164911	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11582703	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11584466	0.97[EUR][1000 genomes]
rs12070900	0.84[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12071627	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12080715	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088338	0.84[EUR][1000 genomes]
rs12090723	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12731675	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12731809	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1323626	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1323627	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1323628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1414367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1535698	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1570528	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs17131699	1.00[ASW][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs2031223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2031224	0.97[EUR][1000 genomes]
rs2104280	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2749735	0.82[EUR][1000 genomes]
rs2783492	0.82[EUR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs2783506	0.82[EUR][1000 genomes]
rs2815408	0.81[EUR][1000 genomes]
rs2815409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2815410	0.93[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2815411	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2815412	0.81[EUR][1000 genomes]
rs2815413	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2815414	0.85[EUR][1000 genomes]
rs4573531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4847407	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4847409	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs4847411	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs485622	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs505531	0.86[EUR][1000 genomes]
rs506556	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs508942	0.96[EUR][1000 genomes]
rs512361	0.97[EUR][1000 genomes]
rs519723	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs523262	0.95[EUR][1000 genomes]
rs546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs556888	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs558667	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs559397	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56303209	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs566743	0.93[EUR][1000 genomes]
rs571212	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs573056	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs581825	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs587754	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs605759	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs615416	0.83[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs629153	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs631966	0.97[EUR][1000 genomes]
rs633789	0.93[CEU][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs637198	0.96[EUR][1000 genomes]
rs641390	0.96[EUR][1000 genomes]
rs6541351	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6541400	0.97[EUR][1000 genomes]
rs658178	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs661566	0.91[EUR][1000 genomes]
rs662546	0.91[EUR][1000 genomes]
rs6657587	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667701	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs667680	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6687359	0.97[EUR][1000 genomes]
rs668944	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs6701250	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs670650	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs671559	0.85[EUR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs698926	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7413775	0.97[EUR][1000 genomes]
rs7519163	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs7525189	0.97[EUR][1000 genomes]
rs7529639	0.89[EUR][1000 genomes]
rs7546661	0.89[EUR][1000 genomes]
rs7551635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs771448	0.88[EUR][1000 genomes]
rs771449	0.89[EUR][1000 genomes]
rs771450	0.89[EUR][1000 genomes]
rs771451	0.89[EUR][1000 genomes]
rs771452	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771453	0.89[EUR][1000 genomes]
rs771456	0.92[EUR][1000 genomes]
rs771457	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771459	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs771460	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771463	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs771464	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771467	0.90[EUR][1000 genomes]
rs771468	0.90[EUR][1000 genomes]
rs771469	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs771471	0.90[EUR][1000 genomes]
rs771472	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771474	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs771475	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs771477	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[EUR][1000 genomes]
rs771480	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs797660	0.87[EUR][1000 genomes]
rs797669	0.90[EUR][1000 genomes]
rs809515	0.89[EUR][1000 genomes]
rs810028	0.90[EUR][1000 genomes]
rs812789	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9432680	0.96[EUR][1000 genomes]
rs9432700	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9432701	0.96[EUR][1000 genomes]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs7555292	RP4-717I23.3	cis	Artery Aorta	GTEx
rs7555292	RP4-717I23.3	cis	lung	GTEx
rs7555292	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs7555292	TMED5	cis	parietal	SCAN
rs7555292	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs7555292	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs7555292	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs7555292	LOC646848	cis	normal skin	skin_eQTL
rs7555292	RP4-717I23.3	cis	Thyroid	GTEx
rs7555292	TMED5	cis	multi-tissue	Pritchard
rs7555292	RP4-717I23.3	cis	Whole Blood	GTEx
rs7555292	TMED5	cis	cerebellum	SCAN
rs7555292	DR1	cis	multi-tissue	Pritchard
rs7555292	LOC646848	cis	multi-tissue	Pritchard
rs7555292	RP4-717I23.3	cis	Artery Tibial	GTEx
rs7555292	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs7555292	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs7555292	RP4-717I23.3	cis	Stomach	GTEx
rs7555292	RP4-717I23.3	cis	Nerve Tibial	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93729000-93790200	Weak transcription	Osteobl	bone
2	chr1:93746600-93789400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:93751600-93794600	Weak transcription	Brain Substantia Nigra	brain
4	chr1:93753000-93803600	Weak transcription	Adipose Nuclei	Adipose
5	chr1:93753200-93806400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:93755400-93802600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:93755400-93803200	Weak transcription	Fetal Thymus	thymus
8	chr1:93755600-93803400	Weak transcription	Fetal Intestine Large	intestine
9	chr1:93755600-93804200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:93755800-93790200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:93755800-93801400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:93756000-93803800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:93765800-93809800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:93767800-93801400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:93768600-93791600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:93768600-93803000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:93770600-93789400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:93770800-93790200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:93772600-93806000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:93779600-93804000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:93780400-93790200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:93783000-93803400	Weak transcription	Left Ventricle	heart
23	chr1:93783800-93789800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:93783800-93801200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:93784400-93804000	Weak transcription	Thymus	Thymus
26	chr1:93786000-93789800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:93786200-93803800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:93786400-93791800	Enhancers	Stomach Mucosa	stomach
29	chr1:93787400-93789600	Strong transcription	Primary T cells from cord blood	blood
30	chr1:93787400-93790400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:93787600-93790000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:93788400-93789600	Weak transcription	HMEC	breast
33	chr1:93788600-93789200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr1:93788600-93789200	Enhancers	Esophagus	oesophagus
35	chr1:93788600-93789400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:93788600-93790400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:93788800-93789200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:93788800-93789400	Enhancers	HSMM	muscle
39	chr1:93788800-93789400	Enhancers	HSMMtube	muscle
40	chr1:93788800-93789600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:93788800-93789800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:93788800-93790200	Enhancers	Hela-S3	cervix
43	chr1:93789000-93790200	Enhancers	NHEK	skin
44	chr1:93789000-93797200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr1:93789000-93803800	Weak transcription	Placenta	Placenta

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