Variant report

Variant	rs771464
Chromosome Location	chr1:93813430-93813431
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr1:93810459-93813430	Hela-S3	cervix:	n/a	n/a
2	FOS	chr1:93813290-93813796	MCF10A-Er-Src	breast:	n/a	n/a
3	CUX1	chr1:93813383-93813753	K562	blood:	n/a	n/a
4	CEBPB	chr1:93813321-93813493	K562	blood:	n/a	n/a
5	CEBPB	chr1:93813249-93813501	IMR90	lung:	n/a	n/a
6	MXI1	chr1:93810253-93813673	SK-N-SH	brain:	n/a	chr1:93812833-93812842

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93711984..93714906-chr1:93812778..93814331,2	K562	blood:
2	chr1:93645217..93647483-chr1:93810016..93813905,4	K562	blood:
3	chr1:93642386..93644618-chr1:93813352..93815941,2	K562	blood:
4	chr1:93811453..93813762-chr1:94372603..94376116,3	K562	blood:
5	chr1:93811133..93814005-chr1:93913050..93915053,2	MCF-7	breast:
6	chr1:93811453..93814121-chr1:94372637..94375148,3	K562	blood:
7	chr1:93768904..93771208-chr1:93812676..93814226,2	MCF-7	breast:
8	chr1:93810887..93813199-chr1:93813270..93816072,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000223745	TF binding region
ENSG00000137942	Chromatin interaction
ENSG00000023909	Chromatin interaction
ENSG00000117500	Chromatin interaction
ENSG00000117505	Chromatin interaction
ENSG00000223745	Chromatin interaction
ENSG00000122483	Chromatin interaction

Extended variants
information (count: 132 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs1000606	0.92[EUR][1000 genomes]
rs10430073	0.92[EUR][1000 genomes]
rs10782958	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1081523	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1081524	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1081525	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1081526	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10874765	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10874767	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10874771	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10874774	0.87[EUR][1000 genomes]
rs10874775	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1088319	0.84[EUR][1000 genomes]
rs11164878	0.81[AMR][1000 genomes]
rs11164882	0.81[AMR][1000 genomes]
rs11164888	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164889	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164890	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11164891	0.89[EUR][1000 genomes]
rs11164906	0.92[EUR][1000 genomes]
rs11164911	0.97[EUR][1000 genomes]
rs11582703	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11584466	0.92[EUR][1000 genomes]
rs12070900	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12071627	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12080715	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12085959	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12090723	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12731675	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12731809	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1323626	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1323627	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1323628	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1414367	0.81[AMR][1000 genomes]
rs1535698	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1535700	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1570528	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2031223	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2031224	0.92[EUR][1000 genomes]
rs2104280	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2484485	0.81[AMR][1000 genomes]
rs2783492	0.81[AMR][1000 genomes]
rs2783498	0.81[AMR][1000 genomes]
rs2783506	0.81[AMR][1000 genomes]
rs2815408	0.81[AMR][1000 genomes]
rs2815409	0.81[AMR][1000 genomes]
rs2815410	0.81[AMR][1000 genomes]
rs2815411	0.81[AMR][1000 genomes]
rs2815414	0.80[EUR][1000 genomes]
rs4573531	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4847239	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4847407	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4847409	0.92[EUR][1000 genomes]
rs4847411	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs485622	0.85[EUR][1000 genomes]
rs488646	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs504810	0.89[EUR][1000 genomes]
rs505531	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs508942	0.90[EUR][1000 genomes]
rs512361	0.92[EUR][1000 genomes]
rs519723	0.88[EUR][1000 genomes]
rs523262	0.90[EUR][1000 genomes]
rs546	0.81[AMR][1000 genomes]
rs556888	0.92[EUR][1000 genomes]
rs558667	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs559397	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56303209	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs566743	0.88[EUR][1000 genomes]
rs571212	0.84[EUR][1000 genomes]
rs587754	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs605759	0.86[EUR][1000 genomes]
rs626714	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs628714	0.89[EUR][1000 genomes]
rs629153	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs631966	0.92[EUR][1000 genomes]
rs633789	0.92[EUR][1000 genomes]
rs637198	0.90[EUR][1000 genomes]
rs641390	0.90[EUR][1000 genomes]
rs6541351	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6541400	0.92[EUR][1000 genomes]
rs658178	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs661566	0.86[EUR][1000 genomes]
rs662546	0.86[EUR][1000 genomes]
rs6657587	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6664886	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6667701	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs667680	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6687359	0.92[EUR][1000 genomes]
rs668944	0.89[EUR][1000 genomes]
rs6701250	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs670650	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs671559	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs693872	0.92[EUR][1000 genomes]
rs698926	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7413775	0.92[EUR][1000 genomes]
rs7519163	0.92[EUR][1000 genomes]
rs7525189	0.92[EUR][1000 genomes]
rs7529639	0.94[EUR][1000 genomes]
rs7546661	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7551635	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7555292	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771448	0.93[EUR][1000 genomes]
rs771449	0.94[EUR][1000 genomes]
rs771450	0.94[EUR][1000 genomes]
rs771451	0.94[EUR][1000 genomes]
rs771452	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771453	0.94[EUR][1000 genomes]
rs771455	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs771456	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771457	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771459	0.94[EUR][1000 genomes]
rs771460	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771463	0.97[EUR][1000 genomes]
rs771466	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771467	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771468	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771469	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771471	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771472	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771474	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771475	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771477	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771480	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs797660	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs797669	0.85[EUR][1000 genomes]
rs809515	0.84[EUR][1000 genomes]
rs810028	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs812789	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9432680	0.91[EUR][1000 genomes]
rs9432700	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9432701	0.91[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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs771464	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs771464	RP4-717I23.3	cis	Thyroid	GTEx
rs771464	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs771464	RP4-717I23.3	cis	Artery Aorta	GTEx
rs771464	RP4-717I23.3	cis	Whole Blood	GTEx
rs771464	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs771464	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs771464	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs771464	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs771464	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs771464	RP4-717I23.3	cis	Stomach	GTEx
rs771464	RP4-717I23.3	cis	lung	GTEx
rs771464	RP4-717I23.3	cis	Artery Tibial	GTEx
rs771464	RP4-717I23.3	cis	Esophagus Muscularis	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	chr1:93810400-93813600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:93810400-93813800	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr1:93810400-93814200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:93810400-93814200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:93810400-93814200	Active TSS	Fetal Intestine Small	intestine
10	chr1:93810400-93814400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:93810400-93814800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:93810400-93814800	Active TSS	Osteobl	bone
13	chr1:93810400-93815000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:93810400-93815000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:93810400-93815000	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:93810400-93815000	Active TSS	A549	lung
17	chr1:93810400-93815200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:93810400-93815200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:93810400-93815200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:93810400-93815200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:93810400-93815200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:93810400-93815200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:93810400-93815200	Active TSS	K562	blood
24	chr1:93810400-93815200	Active TSS	NHLF	lung
25	chr1:93810400-93815400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:93810400-93815400	Active TSS	Fetal Intestine Large	intestine
27	chr1:93810400-93815400	Active TSS	HSMM	muscle
28	chr1:93810400-93815600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:93810400-93815600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:93810400-93815600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:93810400-93816200	Active TSS	HSMMtube	muscle
32	chr1:93810600-93813600	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:93810600-93813800	Active TSS	Placenta Amnion	Placenta Amnion
34	chr1:93810600-93813800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr1:93810600-93814000	Active TSS	Brain Substantia Nigra	brain
36	chr1:93810600-93814200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:93810600-93814200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:93810600-93814200	Active TSS	Primary T cells fromperipheralblood	blood
39	chr1:93810600-93814200	Active TSS	Psoas Muscle	Psoas
40	chr1:93810600-93814200	Active TSS	Right Ventricle	heart
41	chr1:93810600-93814400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:93810600-93814400	Active TSS	Placenta	Placenta
43	chr1:93810600-93814600	Active TSS	Fetal Brain Female	brain
44	chr1:93810600-93814600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr1:93810600-93814800	Active TSS	Brain Germinal Matrix	brain
46	chr1:93810600-93815200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr1:93810600-93815200	Active TSS	Fetal Stomach	stomach
48	chr1:93810600-93815200	Active TSS	NHDF-Ad	bronchial
49	chr1:93810600-93815600	Active TSS	Fetal Muscle Leg	muscle
50	chr1:93810600-93815600	Active TSS	Fetal Thymus	thymus

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