Variant report

Variant	rs7594278
Chromosome Location	chr2:46604593-46604594
allele	G/T
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	POLR2A	chr2:46602784-46612387	HepG2	liver:	n/a	n/a
2	CTCF	chr2:46604456-46604656	GM12878	blood:	n/a	chr2:46604516-46604534
3	CTCF	chr2:46604316-46604757	MCF-7	breast:	n/a	chr2:46604516-46604534
4	POLR2A	chr2:46603726-46605552	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr2:46604394-46604607	SK-N-SH_RA	brain:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
6	CTCF	chr2:46604580-46604730	A549	lung:	n/a	n/a
7	CTCF	chr2:46604405-46604748	K562	blood:	n/a	chr2:46604516-46604534
8	CTCF	chr2:46604444-46604650	K562	blood:	n/a	chr2:46604516-46604534
9	CTCF	chr2:46604460-46604610	NHDF-neo	bronchial:	n/a	chr2:46604516-46604534
10	RAD21	chr2:46604416-46604609	K562	blood:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
11	CTCF	chr2:46604479-46604600	MCF-7	breast:	n/a	chr2:46604516-46604534
12	RAD21	chr2:46604431-46604646	HepG2	liver:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
13	CTCF	chr2:46604480-46604630	HCFaa	heart:	n/a	chr2:46604516-46604534
14	CTCF	chr2:46604447-46604643	Medullo	brain:	n/a	chr2:46604516-46604534
15	RAD21	chr2:46604407-46604639	H1-hESC	embryonic stem cell:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
16	POLR2A	chr2:46602319-46619222	K562	blood:	n/a	n/a
17	CTCF	chr2:46604458-46604610	K562	blood:	n/a	chr2:46604516-46604534
18	CTCF	chr2:46604460-46604610	HRPEpiC	eye:	n/a	chr2:46604516-46604534
19	CTCF	chr2:46604480-46604630	HCM	heart:	n/a	chr2:46604516-46604534
20	RAD21	chr2:46604339-46604748	MCF-7	breast:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
21	CTCF	chr2:46604500-46604650	GM12873	blood:	n/a	chr2:46604516-46604534
22	CTCF	chr2:46604480-46604598	Hela-S3	cervix:	n/a	chr2:46604516-46604534
23	CTCF	chr2:46604458-46604656	Fibrobl	skin:	n/a	chr2:46604516-46604534
24	RAD21	chr2:46604256-46604686	A549	lung:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
25	POLR2A	chr2:46604491-46604651	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr2:46604444-46604625	A549	lung:	n/a	chr2:46604516-46604534
27	CTCF	chr2:46604480-46604630	GM12873	blood:	n/a	chr2:46604516-46604534
28	CTCF	chr2:46604362-46604685	K562	blood:	n/a	chr2:46604516-46604534
29	RAD21	chr2:46603851-46604946	SK-N-SH	brain:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
30	CTCF	chr2:46604449-46604629	MCF-7	breast:	n/a	chr2:46604516-46604534
31	RAD21	chr2:46604350-46604623	SK-N-SH_RA	brain:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
32	RAD21	chr2:46604348-46604709	H1-hESC	embryonic stem cell:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
33	CTCF	chr2:46604459-46604620	GM12892	blood:	n/a	chr2:46604516-46604534
34	CTCF	chr2:46604295-46604636	A549	lung:	n/a	chr2:46604516-46604534
35	POLR2A	chr2:46604183-46604634	A549	lung:	n/a	n/a
36	RAD21	chr2:46604320-46604733	MCF-7	breast:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
37	CTCF	chr2:46604448-46604639	MCF-7	breast:	n/a	chr2:46604516-46604534
38	RAD21	chr2:46604372-46604765	H1-hESC	embryonic stem cell:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
39	CTCF	chr2:46604435-46604641	MCF-7	breast:	n/a	chr2:46604516-46604534
40	SMC3	chr2:46604413-46604628	K562	blood:	n/a	n/a
41	CTCF	chr2:46604500-46604650	NHDF-neo	bronchial:	n/a	chr2:46604516-46604534
42	CTCF	chr2:46604500-46604650	HVMF	connective:	n/a	chr2:46604516-46604534
43	RAD21	chr2:46604444-46604662	A549	lung:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
44	CTCF	chr2:46604460-46604610	A549	lung:	n/a	chr2:46604516-46604534
45	CTCF	chr2:46604520-46604670	Caco-2	colon:	n/a	n/a
46	RAD21	chr2:46604389-46604599	K562	blood:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
47	CTCF	chr2:46604407-46604627	A549	lung:	n/a	chr2:46604516-46604534
48	CTCF	chr2:46604419-46604646	H1-hESC	embryonic stem cell:	n/a	chr2:46604516-46604534
49	RAD21	chr2:46604267-46604771	A549	lung:	n/a	chr2:46604514-46604533 chr2:46604513-46604525 chr2:46604518-46604532
50	CTCF	chr2:46604404-46604608	A549	lung:	n/a	chr2:46604516-46604534

No.	Distal block	Cell Line	Cell type
1	chr2:46603996..46606456-chr2:46616459..46618582,2	K562	blood:
2	chr2:46602852..46605080-chr2:46635870..46638322,2	MCF-7	breast:
3	chr2:46598299..46600622-chr2:46603108..46604803,2	K562	blood:
4	chr2:46600582..46603606-chr2:46603926..46607048,4	K562	blood:

Variant related genes	Relation type
EPAS1	TF binding region
ENSG00000116016	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10178633	0.85[CEU][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.85[AMR][1000 genomes]
rs11675232	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11675328	0.90[AMR][1000 genomes]
rs11675441	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11678465	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11678817	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11681242	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11686705	0.92[AMR][1000 genomes]
rs11690951	0.89[CEU][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11691694	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11692911	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11693596	0.89[AMR][1000 genomes]
rs11693754	0.92[AMR][1000 genomes]
rs11694193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467821	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13006131	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13019268	0.85[CHB][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1530622	0.81[CEU][hapmap];0.83[CHB][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1530631	0.81[CEU][hapmap]
rs1868092	0.81[CEU][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1868093	0.81[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1868094	0.81[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35145595	0.82[EUR][1000 genomes]
rs35193335	0.81[ASN][1000 genomes]
rs3768730	0.89[CEU][hapmap]
rs4953356	0.81[CEU][hapmap]
rs4953358	0.81[CEU][hapmap]
rs4953359	0.84[CEU][hapmap]
rs55826825	0.90[AMR][1000 genomes]
rs56161503	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56768253	0.80[EUR][1000 genomes]
rs59034065	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62138871	0.89[AMR][1000 genomes]
rs6707241	0.81[CEU][hapmap]
rs6735812	0.81[CEU][hapmap]
rs6740096	0.80[CEU][hapmap]
rs6743991	0.81[CEU][hapmap]
rs6756667	0.81[CEU][hapmap]
rs7557402	0.92[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7567582	0.96[CEU][hapmap];0.83[CHB][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7568285	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7571218	0.88[GIH][hapmap]
rs7583088	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7583392	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7591548	0.90[AMR][1000 genomes]
rs7594912	0.85[CEU][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7598371	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7606559	0.96[CEU][hapmap];0.83[CHB][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46573200-46613000	Strong transcription	Hela-S3	cervix
2	chr2:46574600-46607200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:46574800-46613000	Weak transcription	HSMM	muscle
4	chr2:46588600-46604800	Weak transcription	Stomach Mucosa	stomach
5	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
6	chr2:46591200-46606400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:46592000-46605000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr2:46592200-46619800	Weak transcription	K562	blood
9	chr2:46592600-46606600	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr2:46592600-46608400	Strong transcription	Osteobl	bone
11	chr2:46592600-46611200	Weak transcription	Primary T cells from cord blood	blood
12	chr2:46592600-46612600	Strong transcription	NHEK	skin
13	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr2:46593600-46615400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:46594000-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:46594400-46615600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr2:46594600-46612800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:46594800-46615400	Strong transcription	Liver	Liver
19	chr2:46594800-46615600	Strong transcription	HUVEC	blood vessel
20	chr2:46595000-46616000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:46596000-46605800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:46596000-46612800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:46596200-46605200	Strong transcription	Ovary	ovary
24	chr2:46597800-46605800	Weak transcription	Fetal Heart	heart
25	chr2:46598200-46605600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:46598800-46604800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:46598800-46604800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:46599200-46606000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:46600600-46605400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:46600600-46612600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:46600800-46608400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:46600800-46609200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:46600800-46614200	Strong transcription	HepG2	liver
34	chr2:46601000-46607400	Strong transcription	HMEC	breast
35	chr2:46601200-46606800	Weak transcription	Psoas Muscle	Psoas
36	chr2:46601600-46605000	Weak transcription	A549	lung
37	chr2:46601800-46616400	Genic enhancers	Placenta	Placenta
38	chr2:46602000-46609800	Strong transcription	Small Intestine	intestine
39	chr2:46602000-46616000	Strong transcription	Pancreas	Pancrea
40	chr2:46602200-46606400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:46602400-46604800	Strong transcription	Colonic Mucosa	Colon
42	chr2:46602400-46606000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:46602400-46608800	Strong transcription	Spleen	Spleen
44	chr2:46602400-46613400	Strong transcription	Fetal Intestine Small	intestine
45	chr2:46602600-46605200	Strong transcription	Esophagus	oesophagus
46	chr2:46602600-46606000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:46602800-46604800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:46602800-46606000	Genic enhancers	Left Ventricle	heart
49	chr2:46603000-46604600	Weak transcription	Right Atrium	heart
50	chr2:46603000-46605000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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