Variant report

Variant	rs771463
Chromosome Location	chr1:93813999-93814000
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:93813851-93814002	K562	blood:	n/a	chr1:93813981-93813994
2	FOS	chr1:93813597-93814416	MCF10A-Er-Src	breast:	n/a	chr1:93814208-93814220 chr1:93814210-93814218
3	BACH1	chr1:93813941-93814009	K562	blood:	n/a	n/a
4	GTF2F1	chr1:93813980-93814064	H1-hESC	embryonic stem cell:	n/a	n/a
5	ARID3A	chr1:93813881-93814116	K562	blood:	n/a	n/a
6	CEBPB	chr1:93813814-93814394	Hela-S3	cervix:	n/a	chr1:93814244-93814253 chr1:93813981-93813994

No.	Distal block	Cell Line	Cell type
1	chr1:93711984..93714906-chr1:93812778..93814331,2	K562	blood:
2	chr1:93642386..93644618-chr1:93813352..93815941,2	K562	blood:
3	chr1:93813688..93816187-chr1:93818806..93820791,2	MCF-7	breast:
4	chr1:93811133..93814005-chr1:93913050..93915053,2	MCF-7	breast:
5	chr1:93811453..93814121-chr1:94372637..94375148,3	K562	blood:
6	chr1:93789973..93792752-chr1:93813733..93815451,2	K562	blood:
7	chr1:93768904..93771208-chr1:93812676..93814226,2	MCF-7	breast:
8	chr1:93810887..93813199-chr1:93813270..93816072,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	TF binding region
ENSG00000023909	Chromatin interaction
ENSG00000137942	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000223745	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1000606	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10430073	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10782958	0.92[EUR][1000 genomes]
rs10782959	0.83[YRI][hapmap]
rs1081523	0.91[EUR][1000 genomes]
rs1081524	0.93[EUR][1000 genomes]
rs1081525	0.95[EUR][1000 genomes]
rs1081526	0.94[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs10874771	0.92[EUR][1000 genomes]
rs10874774	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10874775	0.97[EUR][1000 genomes]
rs1088319	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164882	0.85[CEU][hapmap]
rs11164888	0.93[EUR][1000 genomes]
rs11164889	0.93[EUR][1000 genomes]
rs11164890	0.93[EUR][1000 genomes]
rs11164891	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11164906	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164911	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11582703	0.92[EUR][1000 genomes]
rs11584466	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807404	1.00[JPT][hapmap]
rs12070900	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs12071627	0.92[EUR][1000 genomes]
rs12080715	0.91[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12090723	0.92[EUR][1000 genomes]
rs12731675	0.92[EUR][1000 genomes]
rs12731809	0.92[EUR][1000 genomes]
rs1323626	0.93[EUR][1000 genomes]
rs1323627	0.92[EUR][1000 genomes]
rs1323628	1.00[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs1414367	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs1535698	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1570528	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2031223	0.97[EUR][1000 genomes]
rs2031224	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2104280	0.90[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap]
rs2783498	0.92[CEU][hapmap]
rs2815409	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs2815410	0.93[CEU][hapmap]
rs2815411	1.00[CEU][hapmap]
rs2815413	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4573531	0.92[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4847407	0.92[EUR][1000 genomes]
rs4847409	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4847411	0.97[EUR][1000 genomes]
rs485622	0.84[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs506556	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs508942	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs512361	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs519723	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs523262	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs546	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs556888	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs558667	0.91[EUR][1000 genomes]
rs559397	0.92[EUR][1000 genomes]
rs56303209	0.92[EUR][1000 genomes]
rs566743	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs571212	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs573056	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs581825	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs587754	0.92[EUR][1000 genomes]
rs589241	0.88[AMR][1000 genomes]
rs605759	0.85[EUR][1000 genomes]
rs615416	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs629153	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs631966	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs633789	0.94[ASW][hapmap];0.93[CEU][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs637198	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs641390	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6541351	0.93[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs6541400	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs658178	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs661566	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs662546	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6657587	0.93[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6667701	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs6687359	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs668944	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6701250	1.00[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs670650	0.90[EUR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs698926	0.96[EUR][1000 genomes]
rs7413775	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7519163	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7525189	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7529639	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546661	0.94[EUR][1000 genomes]
rs7551635	0.92[EUR][1000 genomes]
rs7555292	1.00[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs771448	0.92[EUR][1000 genomes]
rs771449	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs771450	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs771451	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs771452	0.94[EUR][1000 genomes]
rs771453	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs771456	0.96[EUR][1000 genomes]
rs771457	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs771459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771460	0.96[EUR][1000 genomes]
rs771464	0.97[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs771467	0.95[EUR][1000 genomes]
rs771468	0.95[EUR][1000 genomes]
rs771469	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs771471	0.95[EUR][1000 genomes]
rs771472	0.94[EUR][1000 genomes]
rs771474	0.94[EUR][1000 genomes]
rs771475	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs771477	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[EUR][1000 genomes]
rs771480	0.94[EUR][1000 genomes]
rs797669	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs809515	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs810028	0.95[EUR][1000 genomes]
rs812789	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9432680	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9432700	0.92[EUR][1000 genomes]
rs9432701	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs771463	RP4-717I23.3	cis	Thyroid	GTEx
rs771463	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs771463	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs771463	RP4-717I23.3	cis	Artery Tibial	GTEx
rs771463	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs771463	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs771463	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs771463	RP4-717I23.3	cis	Whole Blood	GTEx
rs771463	TMED5	cis	multi-tissue	Pritchard
rs771463	RP4-717I23.3	cis	Artery Aorta	GTEx
rs771463	LOC646848	cis	multi-tissue	Pritchard
rs771463	TMED5	cis	parietal	SCAN
rs771463	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs771463	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs771463	DR1	cis	multi-tissue	Pritchard
rs771463	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs771463	TMED5	cis	cerebellum	SCAN
rs771463	RP4-717I23.3	cis	Stomach	GTEx
rs771463	RP4-717I23.3	cis	lung	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93809800-93817200	Active TSS	GM12878-XiMat	blood
2	chr1:93810000-93815400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:93810200-93814000	Active TSS	Hela-S3	cervix
4	chr1:93810200-93815600	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:93810400-93814200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:93810400-93814200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:93810400-93814200	Active TSS	Fetal Intestine Small	intestine
8	chr1:93810400-93814400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:93810400-93814800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:93810400-93814800	Active TSS	Osteobl	bone
11	chr1:93810400-93815000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:93810400-93815000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:93810400-93815000	Active TSS	Stomach Smooth Muscle	stomach
14	chr1:93810400-93815000	Active TSS	A549	lung
15	chr1:93810400-93815200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:93810400-93815200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:93810400-93815200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:93810400-93815200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:93810400-93815200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:93810400-93815200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:93810400-93815200	Active TSS	K562	blood
22	chr1:93810400-93815200	Active TSS	NHLF	lung
23	chr1:93810400-93815400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:93810400-93815400	Active TSS	Fetal Intestine Large	intestine
25	chr1:93810400-93815400	Active TSS	HSMM	muscle
26	chr1:93810400-93815600	Active TSS	H1 Cell Line	embryonic stem cell
27	chr1:93810400-93815600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:93810400-93815600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:93810400-93816200	Active TSS	HSMMtube	muscle
30	chr1:93810600-93814000	Active TSS	Brain Substantia Nigra	brain
31	chr1:93810600-93814200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:93810600-93814200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:93810600-93814200	Active TSS	Primary T cells fromperipheralblood	blood
34	chr1:93810600-93814200	Active TSS	Psoas Muscle	Psoas
35	chr1:93810600-93814200	Active TSS	Right Ventricle	heart
36	chr1:93810600-93814400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:93810600-93814400	Active TSS	Placenta	Placenta
38	chr1:93810600-93814600	Active TSS	Fetal Brain Female	brain
39	chr1:93810600-93814600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr1:93810600-93814800	Active TSS	Brain Germinal Matrix	brain
41	chr1:93810600-93815200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr1:93810600-93815200	Active TSS	Fetal Stomach	stomach
43	chr1:93810600-93815200	Active TSS	NHDF-Ad	bronchial
44	chr1:93810600-93815600	Active TSS	Fetal Muscle Leg	muscle
45	chr1:93810600-93815600	Active TSS	Fetal Thymus	thymus
46	chr1:93810600-93815600	Active TSS	Right Atrium	heart
47	chr1:93810600-93815800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:93810600-93815800	Active TSS	Thymus	Thymus
49	chr1:93810800-93814000	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr1:93810800-93814000	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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