Variant report

Variant	rs3924635
Chromosome Location	chr4:10658922-10658923
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	ZNF217	chr4:10657698-10659439	MCF-7	breast:	n/a	n/a
2	GATA3	chr4:10658662-10659027	T-47D	breast:	n/a	chr4:10658807-10658815
3	CEBPB	chr4:10657582-10659129	HCT-116	colon:	n/a	n/a
4	GATA3	chr4:10658513-10659168	SK-N-SH	brain:	n/a	chr4:10658807-10658815
5	HDAC2	chr4:10658609-10659010	MCF-7	breast:	n/a	n/a
6	GATA3	chr4:10658587-10659030	T-47D	breast:	n/a	chr4:10658807-10658815
7	HDAC2	chr4:10658607-10659017	MCF-7	breast:	n/a	n/a
8	TCF7L2	chr4:10658628-10658991	MCF-7	breast:	n/a	n/a
9	FOSL2	chr4:10658710-10658997	MCF-7	breast:	n/a	n/a
10	CBX3	chr4:10658540-10659132	HCT-116	colon:	n/a	n/a
11	GATA3	chr4:10658611-10659119	MCF-7	breast:	n/a	chr4:10658807-10658815
12	GATA3	chr4:10657425-10659223	MCF-7	breast:	n/a	chr4:10658807-10658815
13	EP300	chr4:10658678-10658934	T-47D	breast:	n/a	n/a
14	CUX1	chr4:10658777-10658966	GM12878	blood:	n/a	n/a
15	NR2F2	chr4:10658671-10659048	MCF-7	breast:	n/a	n/a
16	GATA3	chr4:10658588-10659036	MCF-7	breast:	n/a	chr4:10658807-10658815
17	EP300	chr4:10658553-10658959	MCF-7	breast:	n/a	n/a
18	SIN3AK20	chr4:10658406-10659071	MCF-7	breast:	n/a	n/a
19	GATA2	chr4:10658643-10658998	HUVEC	blood vessel:	n/a	n/a
20	FOXM1	chr4:10658700-10658994	MCF-7	breast:	n/a	n/a
21	SIN3AK20	chr4:10658609-10659146	HCT-116	colon:	n/a	n/a
22	GATA3	chr4:10658688-10659074	MCF-7	breast:	n/a	chr4:10658807-10658815
23	FOSL1	chr4:10658508-10659119	HCT-116	colon:	n/a	n/a
24	JUND	chr4:10658685-10659134	MCF-7	breast:	n/a	n/a
25	JUND	chr4:10658492-10659066	HCT-116	colon:	n/a	n/a
26	SP1	chr4:10658505-10659164	HCT-116	colon:	n/a	n/a
27	JUND	chr4:10658607-10659171	HCT-116	colon:	n/a	n/a
28	SP1	chr4:10658426-10659262	HCT-116	colon:	n/a	n/a
29	GATA3	chr4:10658529-10659070	SK-N-SH	brain:	n/a	chr4:10658807-10658815
30	CEBPB	chr4:10658663-10658983	MCF-7	breast:	n/a	n/a
31	POLR2A	chr4:10658633-10658958	HCT-116	colon:	n/a	n/a
32	SIN3AK20	chr4:10658536-10659126	MCF-7	breast:	n/a	n/a
33	FOSL1	chr4:10658491-10659199	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
CLNK	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10009156	0.92[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes]
rs10033332	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs10516206	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs12644550	0.81[EUR][1000 genomes]
rs12644618	0.81[EUR][1000 genomes]
rs12650571	0.81[EUR][1000 genomes]
rs13144136	0.91[CEU][hapmap];0.83[CHB][hapmap];0.98[EUR][1000 genomes]
rs28720725	0.86[EUR][1000 genomes]
rs35699234	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36124084	0.80[EUR][1000 genomes]
rs4331770	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4449408	0.81[EUR][1000 genomes]
rs4582144	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs4697643	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4697644	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4697771	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6820441	0.81[EUR][1000 genomes]
rs6822578	0.81[EUR][1000 genomes]
rs6823132	0.83[CEU][hapmap]
rs6836007	0.80[EUR][1000 genomes]
rs6836615	0.99[EUR][1000 genomes]
rs6842006	0.81[EUR][1000 genomes]
rs6855114	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7691659	0.81[EUR][1000 genomes]
rs7696539	0.81[EUR][1000 genomes]
rs9683460	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9790471	0.96[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
2	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
4	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
5	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
7	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
9	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
10	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
11	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
12	nsv593727	chr4:10397327-10694991	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv829860	chr4:10598743-10764854	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10643400-10665600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr4:10656800-10659200	Weak transcription	Fetal Thymus	thymus
3	chr4:10657000-10659400	Enhancers	NH-A	brain
4	chr4:10657600-10659000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr4:10657600-10659200	Enhancers	NHEK	skin
6	chr4:10657600-10659600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:10657800-10659400	Enhancers	HMEC	breast
8	chr4:10657800-10659400	Enhancers	NHLF	lung
9	chr4:10658000-10659800	Enhancers	HUVEC	blood vessel
10	chr4:10658200-10659200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:10658200-10659400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:10658200-10660000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr4:10658200-10660200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr4:10658200-10660800	Enhancers	Brain Germinal Matrix	brain
15	chr4:10658400-10659000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:10658400-10659200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:10658400-10659400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:10658400-10659400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr4:10658400-10659600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr4:10658400-10660400	Enhancers	Fetal Lung	lung
21	chr4:10658600-10659000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:10658800-10659000	Flanking Active TSS	GM12878-XiMat	blood
23	chr4:10658800-10659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:10658800-10659400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:10658800-10659400	Active TSS	Pancreatic Islets	Pancreatic Islet

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