Variant report

Variant	rs12646031
Chromosome Location	chr4:74573507-74573508
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	GATA3	chr4:74573498-74574086	MCF-7	breast:	n/a	chr4:74573790-74573798 chr4:74573786-74573802
2	TCF12	chr4:74573494-74574171	ECC-1	luminal epithelium:	n/a	n/a
3	SP1	chr4:74573450-74574183	HCT-116	colon:	n/a	n/a
4	TCF7L2	chr4:74573288-74573863	Hela-S3	cervix:	n/a	chr4:74573820-74573829
5	JUN	chr4:74573153-74574729	K562	blood:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
6	GATA2	chr4:74573499-74573954	K562	blood:	n/a	chr4:74573786-74573802
7	FOSL1	chr4:74573488-74574123	HCT-116	colon:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
8	FOSL2	chr4:74573416-74574160	A549	lung:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
9	ZKSCAN1	chr4:74573053-74573941	Hela-S3	cervix:	n/a	n/a
10	TCF12	chr4:74573448-74574168	A549	lung:	n/a	n/a
11	KAP1	chr4:74573187-74574372	HEK293	kidney:	n/a	chr4:74573821-74573830
12	JUND	chr4:74573476-74574133	HCT-116	colon:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
13	JUND	chr4:74573446-74574084	SK-N-SH	brain:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
14	PBX3	chr4:74573446-74574034	SK-N-SH	brain:	n/a	n/a
15	EP300	chr4:74572989-74574204	ECC-1	luminal epithelium:	n/a	chr4:74573930-74573944 chr4:74573945-74573959 chr4:74573889-74573898
16	FOSL2	chr4:74573461-74574186	SK-N-SH	brain:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
17	TFAP2C	chr4:74573315-74574268	Hela-S3	cervix:	n/a	n/a
18	JUND	chr4:74573384-74574149	SK-N-SH	brain:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
19	CEBPB	chr4:74573503-74574075	HCT-116	colon:	n/a	n/a
20	GATA3	chr4:74573072-74574148	SK-N-SH	brain:	n/a	chr4:74573790-74573798 chr4:74573786-74573802
21	TCF12	chr4:74573153-74574094	SK-N-SH	brain:	n/a	n/a
22	FOS	chr4:74573414-74574312	HUVEC	blood vessel:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829 chr4:74573818-74573829
23	RCOR1	chr4:74573021-74573992	K562	blood:	n/a	n/a
24	GATA1	chr4:74573078-74574293	PBDE	blood:	n/a	chr4:74573786-74573802
25	JUND	chr4:74573434-74574047	K562	blood:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
26	NR2F2	chr4:74573447-74574139	K562	blood:	n/a	n/a
27	SP1	chr4:74573466-74574179	HCT-116	colon:	n/a	n/a
28	JUND	chr4:74572990-74574242	SK-N-SH	brain:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
29	EP300	chr4:74573327-74574208	SK-N-SH	brain:	n/a	chr4:74573930-74573944 chr4:74573945-74573959 chr4:74573889-74573898
30	ARID3A	chr4:74573481-74574030	K562	blood:	n/a	n/a
31	TCF12	chr4:74573070-74574163	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr4:74573495-74574056	PANC-1	pancreas:	n/a	n/a
33	FOSL1	chr4:74573432-74574150	HCT-116	colon:	n/a	chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573819-74573829 chr4:74573820-74573829 chr4:74573819-74573829
34	GATA3	chr4:74573117-74574241	SK-N-SH	brain:	n/a	chr4:74573790-74573798 chr4:74573786-74573802
35	GATA3	chr4:74573443-74574206	A549	lung:	n/a	chr4:74573790-74573798 chr4:74573786-74573802
36	NFIC	chr4:74573427-74574172	ECC-1	luminal epithelium:	n/a	n/a
37	GATA2	chr4:74573252-74574276	HUVEC	blood vessel:	n/a	chr4:74573786-74573802
38	TCF7L2	chr4:74573139-74574205	PANC-1	pancreas:	n/a	chr4:74573820-74573829
39	EP300	chr4:74573382-74574215	SK-N-SH	brain:	n/a	chr4:74573930-74573944 chr4:74573945-74573959 chr4:74573889-74573898
40	NFIC	chr4:74573227-74574205	SK-N-SH	brain:	n/a	n/a
41	SP1	chr4:74573495-74574092	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:74572069..74574154-chr4:75022228..75024070,2	MCF-7	breast:
2	chr4:74571713..74573594-chr4:74589343..74591305,2	K562	blood:
3	chr4:74571666..74575174-chr4:74576525..74580241,3	K562	blood:
4	chr4:74569886..74571730-chr4:74572414..74575134,2	MCF-7	breast:
5	chr4:74561984..74564157-chr4:74572990..74575349,2	K562	blood:
6	chr4:74572825..74575404-chr4:74599407..74602314,2	K562	blood:
7	chr4:74570843..74573608-chr4:74593259..74594924,2	K562	blood:
8	chr4:74573010..74574962-chr4:74920043..74922609,2	K562	blood:

Variant related genes	Relation type
ENSG00000228277	TF binding region
ENSG00000248848	Chromatin interaction
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10025373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029200	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10938089	0.96[ASN][1000 genomes]
rs10938091	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11722921	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11938646	0.96[ASN][1000 genomes]
rs1247605	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247607	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247608	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247611	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247620	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247633	0.96[ASN][1000 genomes]
rs1247634	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1247635	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1247639	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1247687	0.98[ASN][1000 genomes]
rs1247689	0.95[ASN][1000 genomes]
rs12508451	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1261935	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642878	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12643076	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12643148	0.98[ASN][1000 genomes]
rs12649614	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1269764	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1269766	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1358594	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1406498	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1528910	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1528912	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528913	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729722	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1745246	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1951702	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951703	0.98[ASN][1000 genomes]
rs1951704	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951705	0.98[ASN][1000 genomes]
rs2091587	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141467	0.98[ASN][1000 genomes]
rs2141468	0.96[ASN][1000 genomes]
rs2178291	0.98[ASN][1000 genomes]
rs2367273	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2886918	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796679	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4127802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259030	0.95[ASN][1000 genomes]
rs4568212	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637366	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4694633	0.98[ASN][1000 genomes]
rs56785010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61101665	0.98[ASN][1000 genomes]
rs6446950	0.87[ASN][1000 genomes]
rs6446951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446953	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6446954	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6818711	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6836038	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857472	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720702	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72865497	0.98[ASN][1000 genomes]
rs72865502	0.98[ASN][1000 genomes]
rs7655660	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7656501	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7656608	0.96[ASN][1000 genomes]
rs7657356	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7657358	0.98[ASN][1000 genomes]
rs7660448	0.96[ASN][1000 genomes]
rs7660923	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7665606	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7678280	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7678307	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7681924	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7681932	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7682745	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7683759	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7689702	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942051	0.98[ASN][1000 genomes]
rs9991585	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012198	chr4:74487793-74621952	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv537139	chr4:74487793-74621952	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1005231	chr4:74555497-74680079	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74566800-74574600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:74566800-74575400	Enhancers	HMEC	breast
3	chr4:74567800-74574000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:74568000-74573800	Enhancers	NHEK	skin
5	chr4:74568000-74574400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:74568200-74574800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:74568200-74574800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:74568400-74574600	Enhancers	NHLF	lung
9	chr4:74569200-74576400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr4:74569800-74576200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:74570000-74575200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:74570400-74573800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:74570400-74573800	Enhancers	Hela-S3	cervix
14	chr4:74570400-74574000	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:74570600-74574000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:74570600-74578600	Enhancers	K562	blood
17	chr4:74570600-74581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:74571000-74573600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:74571000-74574200	Weak transcription	Pancreas	Pancrea
20	chr4:74571200-74573600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:74571400-74573800	Enhancers	HUVEC	blood vessel
22	chr4:74571400-74574000	Weak transcription	Primary B cells from cord blood	blood
23	chr4:74571400-74574600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:74571400-74574600	Enhancers	NHDF-Ad	bronchial
25	chr4:74571400-74574600	Enhancers	Osteobl	bone
26	chr4:74571600-74573600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:74572400-74574000	Weak transcription	HSMMtube	muscle
28	chr4:74572400-74574400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:74572600-74574200	Enhancers	NH-A	brain
30	chr4:74572800-74573600	Enhancers	Dnd41	blood
31	chr4:74572800-74575600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:74572800-74576000	Enhancers	Primary hematopoietic stem cells	blood
33	chr4:74573000-74574400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:74573000-74574400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr4:74573000-74574400	Flanking Active TSS	A549	lung
36	chr4:74573200-74573600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:74573200-74573600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:74573200-74573600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:74573200-74573800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:74573200-74573800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:74573200-74573800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:74573200-74573800	Enhancers	Duodenum Mucosa	Duodenum
43	chr4:74573200-74574000	Enhancers	Aorta	Aorta
44	chr4:74573200-74574400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr4:74573200-74574400	Enhancers	Fetal Thymus	thymus
46	chr4:74573200-74574400	Enhancers	Left Ventricle	heart
47	chr4:74573200-74574400	Enhancers	Thymus	Thymus
48	chr4:74573200-74574400	Enhancers	HSMM	muscle
49	chr4:74573200-74574400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr4:74573200-74576200	Enhancers	Primary monocytes fromperipheralblood	blood

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