Variant report

Variant	rs10948862
Chromosome Location	chr6:54711471-54711472
allele	A/C
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	chr6:54711212-54711677	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr6:54711334-54711603	HCT-116	colon:	n/a	n/a
3	POLR2A	chr6:54711091-54711664	H1-hESC	embryonic stem cell:	n/a	n/a
4	TAF1	chr6:54711126-54711720	MCF-7	breast:	n/a	n/a
5	POLR2A	chr6:54710974-54713675	Hela-S3	cervix:	n/a	n/a
6	CHD2	chr6:54711112-54713044	Hela-S3	cervix:	n/a	chr6:54711229-54711239
7	POLR2A	chr6:54710993-54712194	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr6:54710926-54712518	HCT-116	colon:	n/a	n/a
9	USF2	chr6:54711349-54711772	H1-hESC	embryonic stem cell:	n/a	chr6:54711727-54711743
10	POLR2A	chr6:54711367-54711627	H1-hESC	embryonic stem cell:	n/a	n/a
11	STAT3	chr6:54711222-54711657	MCF10A-Er-Src	breast:	n/a	chr6:54711525-54711537 chr6:54711520-54711532
12	MYC	chr6:54711187-54711477	H1-hESC	embryonic stem cell:	n/a	chr6:54711427-54711437
13	POLR2A	chr6:54711101-54712033	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr6:54710924-54711875	MCF-7	breast:	n/a	n/a
15	STAT1	chr6:54711042-54713361	Hela-S3	cervix:	n/a	chr6:54712038-54712045 chr6:54712078-54712087 chr6:54712079-54712088 chr6:54711525-54711537 chr6:54712079-54712087 chr6:54713023-54713037 chr6:54712073-54712093 chr6:54711520-54711532 chr6:54711993-54712005 chr6:54712073-54712093 chr6:54713026-54713034 chr6:54712077-54712088 chr6:54713165-54713173
16	ZNF143	chr6:54711161-54712141	H1-hESC	embryonic stem cell:	n/a	chr6:54711986-54712004 chr6:54711517-54711535 chr6:54711259-54711268 chr6:54711521-54711539 chr6:54711736-54711746
17	E2F4	chr6:54711195-54712148	MCF10A-Er-Src	breast:	n/a	chr6:54711423-54711435 chr6:54711595-54711604 chr6:54711529-54711544 chr6:54711736-54711745 chr6:54711459-54711468
18	SMARCC1	chr6:54711045-54713431	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr6:54711168-54711646	MCF10A-Er-Src	breast:	n/a	chr6:54711525-54711537 chr6:54711520-54711532
20	TAF7	chr6:54711315-54711727	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr6:54710957-54713446	Hela-S3	cervix:	n/a	chr6:54711427-54711437
22	TCF12	chr6:54710972-54712270	ECC-1	luminal epithelium:	n/a	n/a
23	SMARCB1	chr6:54710981-54712318	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr6:54711440-54711524	MCF-7	breast:	n/a	n/a
25	CTCF	chr6:54711400-54711550	HMEC	breast:	n/a	chr6:54711428-54711441
26	POLR2A	chr6:54711104-54711756	ECC-1	luminal epithelium:	n/a	n/a
27	MXI1	chr6:54711289-54711489	H1-hESC	embryonic stem cell:	n/a	n/a
28	HDAC2	chr6:54711036-54712299	MCF-7	breast:	n/a	chr6:54711294-54711308
29	CTBP2	chr6:54711055-54712274	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr6:54710988-54712411	Hela-S3	cervix:	n/a	chr6:54711672-54711686
31	SIN3AK20	chr6:54710850-54713528	MCF-7	breast:	n/a	n/a
32	MYC	chr6:54711251-54711518	MCF10A-Er-Src	breast:	n/a	chr6:54711427-54711437
33	REST	chr6:54711052-54711667	MCF-7	breast:	n/a	chr6:54711484-54711504 chr6:54711209-54711218
34	MXI1	chr6:54711059-54713305	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr6:54711420-54711570	SAEC	small airway:	n/a	chr6:54711428-54711441
36	MYC	chr6:54711370-54711483	MCF-7	breast:	n/a	chr6:54711427-54711437
37	EP300	chr6:54711198-54711680	T-47D	breast:	n/a	chr6:54711595-54711604 chr6:54711578-54711587 chr6:54711581-54711597 chr6:54711583-54711599
38	RCOR1	chr6:54711049-54712070	Hela-S3	cervix:	n/a	n/a
39	TAF1	chr6:54710999-54712164	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr6:54711064-54713478	MCF10A-Er-Src	breast:	n/a	n/a
41	KAP1	chr6:54710888-54712803	HEK293	kidney:	n/a	n/a
42	CTCF	chr6:54711389-54711524	MCF-7	breast:	n/a	chr6:54711428-54711441
43	ZKSCAN1	chr6:54711156-54711917	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr6:54711003-54712273	MCF-7	breast:	n/a	n/a
45	MAFK	chr6:54711334-54711603	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:54710891-54712384	MCF-7	breast:	n/a	n/a
47	FOS	chr6:54711293-54711534	MCF10A-Er-Src	breast:	n/a	n/a
48	NFIC	chr6:54711188-54711735	ECC-1	luminal epithelium:	n/a	n/a
49	CTCF	chr6:54711380-54711482	MCF-7	breast:	n/a	chr6:54711428-54711441
50	FOS	chr6:54711313-54711590	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:54711429-54711479	HIPEpiC	eye:	n/a
2	chr6:54711471-54711521	NB4	blood:	n/a
3	chr6:54711471-54711521	SAEC	small airway:	n/a
4	chr6:54711429-54711479	NH-A	brain:	n/a
5	chr6:54711429-54711479	GM12892	blood:	n/a
6	chr6:54711429-54711479	HNPCEpiC	eye:	n/a
7	chr6:54711471-54711521	ovcar-3	ovarian:	n/a
8	chr6:54711429-54711479	HCF	heart:	n/a
9	chr6:54711429-54711479	HL-60	blood:	n/a
10	chr6:54711429-54711479	BJ	skin:	n/a
11	chr6:54711471-54711521	SK-N-SH	brain:	n/a
12	chr6:54711471-54711521	IMR90	lung:	fetal
13	chr6:54711429-54711479	LNCaP	prostate:	n/a
14	chr6:54711471-54711521	NT2-D1	testis:	n/a
15	chr6:54711471-54711521	AG04449	skin:	fetal
16	chr6:54711429-54711479	GM19239	blood:	n/a
17	chr6:54711429-54711479	HRPEpiC	eye:	n/a
18	chr6:54711429-54711479	PrEC	prostate:	n/a
19	chr6:54711471-54711521	NH-A	brain:	n/a
20	chr6:54711471-54711521	AoSMC	blood vessel:	n/a
21	chr6:54711471-54711521	GM19239	blood:	n/a
22	chr6:54711471-54711521	CMK	blood:	n/a
23	chr6:54711471-54711521	Hepatocyte	liver:	n/a
24	chr6:54711429-54711479	IMR90	lung:	fetal
25	chr6:54711471-54711521	Jurkat	blood:	n/a
26	chr6:54711471-54711521	HL-60	blood:	n/a
27	chr6:54711429-54711479	Hela-S3	cervix:	n/a
28	chr6:54711429-54711479	A549	lung:	n/a
29	chr6:54711429-54711479	AG10803	skin:	n/a
30	chr6:54711429-54711479	HEK293	kidney:	embryo
31	chr6:54711429-54711479	HCT-116	colon:	n/a
32	chr6:54711429-54711479	SAEC	small airway:	n/a
33	chr6:54711429-54711479	GM12891	blood:	n/a
34	chr6:54711429-54711479	HCM	heart:	n/a
35	chr6:54711429-54711479	U87	brain:	n/a
36	chr6:54711429-54711479	HepG2	liver:	n/a
37	chr6:54711429-54711479	AG04449	skin:	fetal
38	chr6:54711429-54711479	H1-hESC	embryonic stem cell:	embryo
39	chr6:54711471-54711521	PFSK-1	brain:	n/a
40	chr6:54711429-54711479	ovcar-3	ovarian:	n/a
41	chr6:54711471-54711521	K562	blood:	n/a
42	chr6:54711471-54711521	GM12892	blood:	n/a
43	chr6:54711429-54711479	SKMC	muscle:	n/a
44	chr6:54711429-54711479	GM12878	blood:	n/a
45	chr6:54711471-54711521	HEK293	kidney:	embryo
46	chr6:54711429-54711479	HRE	kidney:	n/a
47	chr6:54711471-54711521	AG09309	skin:	n/a
48	chr6:54711471-54711521	HepG2	liver:	n/a
49	chr6:54711429-54711479	HUVEC	blood vessel:	n/a
50	chr6:54711429-54711479	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:16129307..16129833-chr6:54711262..54711766,2	Hela-S3	cervix:
2	chr14:65876592..65878564-chr6:54710365..54711981,2	MCF-7	breast:
3	chr6:54633061..54636995-chr6:54710354..54713223,5	MCF-7	breast:

Variant related genes	Relation type
FAM83B	TF binding region
FAM83B	CpG island
ENSG00000033170	Chromatin interaction
ENSG00000220635	Chromatin interaction
ENSG00000007944	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10807484	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10807485	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10948864	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12191299	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12191386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12195438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12196314	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs12199827	0.88[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap]
rs12201892	0.83[ASN][1000 genomes]
rs12202062	0.83[ASN][1000 genomes]
rs12203709	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[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12205222	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12205372	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs12207559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12216039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12216049	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1393778	0.81[AMR][1000 genomes]
rs1393779	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs1910357	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2270989	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs34713378	0.83[ASN][1000 genomes]
rs4712075	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[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62412605	0.84[ASN][1000 genomes]
rs62412647	0.81[EUR][1000 genomes]
rs6908745	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911198	0.84[CHB][hapmap];0.96[CHD][hapmap]
rs6938005	0.80[LWK][hapmap]
rs72957572	0.84[ASN][1000 genomes]
rs7747352	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760490	0.84[ASN][1000 genomes]
rs9296769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464148	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9464149	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475005	0.91[CEU][hapmap]
rs9475029	0.85[ASN][1000 genomes]
rs9475038	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475039	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475040	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475041	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475045	0.87[ASN][1000 genomes]
rs9475046	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10948862	ICK	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54709000-54713400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:54709000-54714200	Active TSS	Duodenum Mucosa	Duodenum
3	chr6:54709800-54713400	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr6:54710200-54711600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54710400-54713200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:54710600-54713800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54710800-54712200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:54710800-54712200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr6:54710800-54712400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr6:54710800-54712400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:54710800-54712400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:54710800-54712600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:54710800-54712600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:54710800-54712800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:54710800-54713000	Active TSS	Fetal Intestine Small	intestine
16	chr6:54710800-54713000	Active TSS	Right Atrium	heart
17	chr6:54710800-54713600	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:54710800-54714400	Active TSS	Colonic Mucosa	Colon
19	chr6:54711000-54711600	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:54711000-54711600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:54711000-54711600	Enhancers	Spleen	Spleen
22	chr6:54711000-54711800	Active TSS	Stomach Mucosa	stomach
23	chr6:54711000-54711800	Bivalent/Poised TSS	NHLF	lung
24	chr6:54711000-54712000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:54711000-54712000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:54711000-54712000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:54711000-54712000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:54711000-54712000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:54711000-54712000	Bivalent/Poised TSS	A549	lung
30	chr6:54711000-54712000	Active TSS	NH-A	brain
31	chr6:54711000-54712000	Bivalent/Poised TSS	Osteobl	bone
32	chr6:54711000-54712200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:54711000-54712200	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr6:54711000-54712200	Active TSS	Fetal Heart	heart
35	chr6:54711000-54712200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr6:54711000-54712200	Bivalent/Poised TSS	Psoas Muscle	Psoas
37	chr6:54711000-54712200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
38	chr6:54711000-54712200	Bivalent/Poised TSS	Thymus	Thymus
39	chr6:54711000-54712200	Active TSS	Hela-S3	cervix
40	chr6:54711000-54712400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:54711000-54712400	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
42	chr6:54711000-54712400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:54711000-54712400	Active TSS	Pancreas	Pancrea
44	chr6:54711000-54712400	Active TSS	Small Intestine	intestine
45	chr6:54711000-54712600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr6:54711000-54712600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr6:54711000-54712600	Bivalent/Poised TSS	Fetal Thymus	thymus
48	chr6:54711000-54712800	Active TSS	Fetal Kidney	kidney
49	chr6:54711000-54713200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr6:54711000-54713200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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