Variant report

Variant	rs6816263
Chromosome Location	chr4:125634675-125634676
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	USF1	chr4:125634448-125634842	SK-N-SH_RA	brain:	n/a	chr4:125634659-125634670
2	CTCF	chr4:125634513-125634761	MCF-7	breast:	n/a	chr4:125634640-125634649
3	CTCF	chr4:125634447-125634792	K562	blood:	n/a	chr4:125634640-125634649
4	POLR2A	chr4:125633127-125634815	GM12892	blood:	n/a	n/a
5	CTCF	chr4:125634560-125634710	MCF-7	breast:	n/a	chr4:125634640-125634649
6	CTCF	chr4:125634374-125634854	IMR90	lung:	n/a	chr4:125634640-125634649
7	CTCF	chr4:125634580-125634730	MCF-7	breast:	n/a	chr4:125634640-125634649
8	JUND	chr4:125634394-125634772	A549	lung:	n/a	n/a
9	CTCF	chr4:125634600-125634750	HAc	cerebellar:	n/a	chr4:125634640-125634649
10	POLR2A	chr4:125633006-125634931	U87	brain:	n/a	n/a
11	CTCF	chr4:125634512-125634755	MCF-7	breast:	n/a	chr4:125634640-125634649
12	POLR2A	chr4:125633070-125634889	HEK293	kidney:	n/a	n/a
13	CTCF	chr4:125634548-125634714	GM19239	blood:	n/a	chr4:125634640-125634649
14	CBX3	chr4:125633914-125634901	K562	blood:	n/a	n/a
15	POLR2A	chr4:125634431-125634739	Hela-S3	cervix:	n/a	n/a
16	TAL1	chr4:125634065-125634854	K562	blood:	n/a	chr4:125634563-125634572
17	HEY1	chr4:125633968-125634877	K562	blood:	n/a	chr4:125634075-125634090
18	UBTF	chr4:125632600-125634787	K562	blood:	n/a	n/a
19	FOXA2	chr4:125634540-125634833	A549	lung:	n/a	n/a
20	MYC	chr4:125634518-125634727	MCF-7	breast:	n/a	n/a
21	CTCF	chr4:125634510-125634751	NHEK	skin:	n/a	chr4:125634640-125634649
22	MAX	chr4:125634426-125634793	K562	blood:	n/a	n/a
23	CTCF	chr4:125634485-125634783	GM12878	blood:	n/a	chr4:125634640-125634649
24	MAX	chr4:125633110-125634869	H1-hESC	embryonic stem cell:	n/a	chr4:125634195-125634205 chr4:125633568-125633578 chr4:125634109-125634118
25	CTCF	chr4:125634560-125634710	GM12870	blood:	n/a	chr4:125634640-125634649
26	CTCF	chr4:125634560-125634710	WERI-Rb-1	eye:	n/a	chr4:125634640-125634649
27	RCOR1	chr4:125633634-125634746	HepG2	liver:	n/a	n/a
28	MAX	chr4:125633014-125634877	ECC-1	luminal epithelium:	n/a	chr4:125634195-125634205 chr4:125633568-125633578 chr4:125634109-125634118
29	CTCF	chr4:125634540-125634690	SK-N-SH_RA	brain:	n/a	chr4:125634640-125634649
30	POLR2A	chr4:125633174-125634709	GM15510	blood:	n/a	n/a
31	RAD21	chr4:125634538-125634741	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr4:125634540-125634690	HepG2	liver:	n/a	chr4:125634640-125634649
33	CHD2	chr4:125633170-125634725	H1-hESC	embryonic stem cell:	n/a	chr4:125633315-125633325 chr4:125633829-125633839
34	ZC3H11A	chr4:125634062-125634834	K562	blood:	n/a	n/a
35	USF1	chr4:125634421-125634835	A549	lung:	n/a	chr4:125634659-125634670
36	BHLHE40	chr4:125633509-125634811	HepG2	liver:	n/a	chr4:125633856-125633872 chr4:125633857-125633873 chr4:125633859-125633875 chr4:125634073-125634089
37	ZNF143	chr4:125634526-125634682	GM12878	blood:	n/a	n/a
38	RCOR1	chr4:125632521-125634889	K562	blood:	n/a	n/a
39	CTCF	chr4:125634540-125634690	HMEC	breast:	n/a	chr4:125634640-125634649
40	POLR2A	chr4:125634481-125634770	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr4:125632483-125634878	K562	blood:	n/a	n/a
42	CTCF	chr4:125634620-125634770	WI-38	lung:	n/a	chr4:125634640-125634649
43	NR2F2	chr4:125634026-125634914	K562	blood:	n/a	n/a
44	CHD2	chr4:125633201-125634784	K562	blood:	n/a	chr4:125633315-125633325 chr4:125633829-125633839
45	POLR2A	chr4:125633691-125634865	K562	blood:	n/a	n/a
46	STAT3	chr4:125634550-125634765	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr4:125634580-125634730	K562	blood:	n/a	chr4:125634640-125634649
48	ATF3	chr4:125634499-125634733	K562	blood:	n/a	n/a
49	POLR2A	chr4:125632690-125634772	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr4:125634072-125635198	K562	blood:	n/a	chr4:125634920-125634928 chr4:125634640-125634649

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:125634632-125634682	HCPEpiC	choroid plexus:	n/a
2	chr4:125634632-125634682	GM19239	blood:	n/a
3	chr4:125634632-125634682	Jurkat	blood:	n/a
4	chr4:125634632-125634682	HPAEpiC	pulmonary alveolar:	n/a
5	chr4:125634632-125634682	CMK	blood:	n/a
6	chr4:125634632-125634682	NH-A	brain:	n/a
7	chr4:125634632-125634682	SKMC	muscle:	n/a
8	chr4:125634632-125634682	A549	lung:	n/a
9	chr4:125634632-125634682	SAEC	small airway:	n/a
10	chr4:125634632-125634682	K562	blood:	n/a
11	chr4:125634632-125634682	HRCEpiC	kidney:	n/a
12	chr4:125634632-125634682	ovcar-3	ovarian:	n/a
13	chr4:125634632-125634682	GM12892	blood:	n/a
14	chr4:125634632-125634682	NB4	blood:	n/a
15	chr4:125634632-125634682	U87	brain:	n/a
16	chr4:125634632-125634682	IMR90	lung:	fetal
17	chr4:125634632-125634682	H1-hESC	embryonic stem cell:	embryo
18	chr4:125634632-125634682	HCF	heart:	n/a
19	chr4:125634632-125634682	HAEpiC	amniotic membrane:	n/a
20	chr4:125634632-125634682	AG09309	skin:	n/a
21	chr4:125634632-125634682	Caco-2	colon:	n/a
22	chr4:125634632-125634682	BE2_C	brain:	n/a
23	chr4:125634632-125634682	SK-N-SH_RA	brain:	n/a
24	chr4:125634632-125634682	HMEC	breast:	n/a
25	chr4:125634632-125634682	MCF-7	breast:	n/a
26	chr4:125634632-125634682	GM12891	blood:	n/a
27	chr4:125634632-125634682	HEEpiC	esophagus:	n/a
28	chr4:125634632-125634682	AG09319	gingival:	n/a
29	chr4:125634632-125634682	Hepatocyte	liver:	n/a
30	chr4:125634632-125634682	HNPCEpiC	eye:	n/a
31	chr4:125634632-125634682	SK-N-MC	brain:	n/a
32	chr4:125634632-125634682	AG10803	skin:	n/a
33	chr4:125634632-125634682	HL-60	blood:	n/a
34	chr4:125634632-125634682	ECC-1	luminal epithelium:	n/a
35	chr4:125634632-125634682	LNCaP	prostate:	n/a
36	chr4:125634632-125634682	AoSMC	blood vessel:	n/a
37	chr4:125634632-125634682	PrEC	prostate:	n/a
38	chr4:125634632-125634682	NHDF-neo	bronchial:	n/a
39	chr4:125634632-125634682	NHBE	bronchial:	n/a
40	chr4:125634632-125634682	AG04450	lung:	fetal
41	chr4:125634632-125634682	RPTEC	kidney:	n/a
42	chr4:125634632-125634682	Hela-S3	cervix:	n/a
43	chr4:125634632-125634682	ProgFib	skin:	n/a
44	chr4:125634632-125634682	SK-N-SH	brain:	n/a
45	chr4:125634632-125634682	HCT-116	colon:	n/a
46	chr4:125634632-125634682	HUVEC	blood vessel:	n/a
47	chr4:125634632-125634682	PFSK-1	brain:	n/a
48	chr4:125634632-125634682	T-47D	breast:	n/a
49	chr4:125634632-125634682	GM06990	blood:	n/a
50	chr4:125634632-125634682	HEK293	kidney:	embryo

No.	Distal block	Cell Line	Cell type
1	chr4:125607408..125609812-chr4:125634396..125636485,2	K562	blood:
2	chr4:125634057..125636507-chr4:125646321..125649119,3	MCF-7	breast:
3	chr4:125355738..125360405-chr4:125631320..125634850,4	MCF-7	breast:

Variant related genes	Relation type
ANKRD50	TF binding region
ANKRD50	CpG island
ENSG00000248506	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10006577	0.82[ASN][1000 genomes]
rs10006893	0.82[ASN][1000 genomes]
rs10018651	0.82[ASN][1000 genomes]
rs10028864	0.84[ASN][1000 genomes]
rs1015968	0.95[ASN][1000 genomes]
rs1016382	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs1016383	0.95[ASN][1000 genomes]
rs10518442	0.97[ASN][1000 genomes]
rs12331436	0.81[ASN][1000 genomes]
rs13104292	0.82[ASN][1000 genomes]
rs13107141	0.94[ASN][1000 genomes]
rs13110120	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs13110982	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs13117832	0.82[ASN][1000 genomes]
rs13130626	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs13144437	0.97[ASN][1000 genomes]
rs13150707	0.88[ASN][1000 genomes]
rs1472290	0.95[ASN][1000 genomes]
rs1495126	0.95[ASN][1000 genomes]
rs1495127	0.82[ASN][1000 genomes]
rs1498024	0.95[ASN][1000 genomes]
rs17008475	0.97[ASN][1000 genomes]
rs17008478	0.97[ASN][1000 genomes]
rs1874748	0.95[ASN][1000 genomes]
rs1995135	0.95[ASN][1000 genomes]
rs2036204	0.84[ASN][1000 genomes]
rs220738	0.82[ASN][1000 genomes]
rs2242378	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs28399027	0.84[ASN][1000 genomes]
rs3172524	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs34348208	0.97[ASN][1000 genomes]
rs34748024	0.95[ASN][1000 genomes]
rs34877613	0.97[ASN][1000 genomes]
rs35053443	0.95[ASN][1000 genomes]
rs35180555	0.95[ASN][1000 genomes]
rs35282937	0.95[ASN][1000 genomes]
rs35333384	0.97[ASN][1000 genomes]
rs35463553	0.95[ASN][1000 genomes]
rs35958270	0.97[ASN][1000 genomes]
rs36177260	0.82[ASN][1000 genomes]
rs3733471	0.82[ASN][1000 genomes]
rs4833999	0.84[ASN][1000 genomes]
rs4834000	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs56902532	0.95[ASN][1000 genomes]
rs59841071	0.95[ASN][1000 genomes]
rs6534448	0.82[ASN][1000 genomes]
rs6815682	0.88[ASN][1000 genomes]
rs6849375	0.88[ASN][1000 genomes]
rs6849813	0.92[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs9307543	0.82[ASN][1000 genomes]
rs9307544	0.82[ASN][1000 genomes]
rs9999425	0.81[ASN][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	esv3343011	chr4:125632527-125635375	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:125630000-125634800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:125630600-125635000	Active TSS	A549	lung
3	chr4:125630600-125635200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr4:125631600-125634800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:125631600-125634800	Active TSS	Aorta	Aorta
6	chr4:125631600-125634800	Active TSS	Ovary	ovary
7	chr4:125631600-125634800	Active TSS	Right Ventricle	heart
8	chr4:125631800-125634800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:125631800-125634800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:125631800-125634800	Active TSS	Stomach Smooth Muscle	stomach
11	chr4:125632000-125635000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:125632200-125634800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr4:125632200-125634800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:125632200-125634800	Active TSS	Fetal Lung	lung
15	chr4:125632200-125634800	Active TSS	Left Ventricle	heart
16	chr4:125632200-125634800	Active TSS	Hela-S3	cervix
17	chr4:125632200-125635000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr4:125632200-125635000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:125632200-125635200	Active TSS	K562	blood
20	chr4:125632400-125634800	Active TSS	Brain Substantia Nigra	brain
21	chr4:125632400-125634800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr4:125632400-125634800	Active TSS	Fetal Kidney	kidney
23	chr4:125632400-125634800	Active TSS	NHEK	skin
24	chr4:125632600-125634800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:125632600-125634800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:125632600-125634800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:125632600-125634800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:125632600-125634800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:125632600-125634800	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:125632800-125634800	Active TSS	Brain Hippocampus Middle	brain
31	chr4:125632800-125635000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr4:125632800-125635000	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr4:125633400-125634800	Active TSS	Primary T cells from cord blood	blood
34	chr4:125633400-125634800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:125634200-125634800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:125634200-125634800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:125634200-125634800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr4:125634200-125634800	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr4:125634200-125634800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr4:125634200-125634800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:125634200-125634800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:125634200-125634800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr4:125634200-125634800	Flanking Active TSS	Liver	Liver
44	chr4:125634200-125634800	Flanking Active TSS	Placenta	Placenta
45	chr4:125634200-125634800	Flanking Active TSS	Pancreas	Pancrea
46	chr4:125634200-125634800	Flanking Active TSS	HMEC	breast
47	chr4:125634200-125634800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr4:125634200-125634800	Flanking Active TSS	NH-A	brain
49	chr4:125634200-125635000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr4:125634200-125635000	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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