Variant report

Variant	rs3797772
Chromosome Location	chr5:179387369-179387370
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	FOXA1	chr5:179387049-179387541	HepG2	liver:	n/a	chr5:179387370-179387382
2	ARID3A	chr5:179387205-179387776	HepG2	liver:	n/a	n/a
3	CEBPB	chr5:179386747-179387610	HepG2	liver:	n/a	chr5:179387295-179387307 chr5:179387380-179387391
4	FOXA2	chr5:179387076-179387544	HepG2	liver:	n/a	chr5:179387370-179387382
5	EP300	chr5:179387170-179387564	HepG2	liver:	n/a	chr5:179387369-179387379 chr5:179387381-179387395
6	CEBPB	chr5:179387297-179387478	A549	lung:	n/a	chr5:179387380-179387391
7	FOXA1	chr5:179387195-179387672	HepG2	liver:	n/a	chr5:179387370-179387382
8	FOXA2	chr5:179386995-179387596	HepG2	liver:	n/a	chr5:179387370-179387382
9	FOXA1	chr5:179387038-179387604	HepG2	liver:	n/a	chr5:179387370-179387382
10	EP300	chr5:179387141-179387469	HepG2	liver:	n/a	chr5:179387369-179387379 chr5:179387381-179387395
11	FOXA1	chr5:179386946-179387659	HepG2	liver:	n/a	chr5:179387370-179387382

No.	Distal block	Cell Line	Cell type
1	chr5:179380756..179384573-chr5:179385269..179388537,4	MCF-7	breast:
2	chr5:179339757..179341423-chr5:179384531..179387426,2	MCF-7	breast:
3	chr5:179387216..179389943-chr5:179396226..179399664,3	MCF-7	breast:
4	chr5:179385954..179387871-chr5:179389769..179391288,2	K562	blood:

Variant related genes	Relation type
RNF130	TF binding region
ENSG00000249412	TF binding region
ENSG00000113269	Chromatin interaction
ENSG00000249412	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2162760	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797769	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179370200-179392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:179373000-179389600	Weak transcription	Fetal Intestine Large	intestine
3	chr5:179373400-179400600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:179373800-179401600	Weak transcription	Colonic Mucosa	Colon
5	chr5:179374600-179387400	Weak transcription	Pancreas	Pancrea
6	chr5:179375400-179392600	Weak transcription	Fetal Kidney	kidney
7	chr5:179376600-179389800	Weak transcription	Placenta	Placenta
8	chr5:179376600-179390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
10	chr5:179379000-179389800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:179379000-179390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:179380000-179392600	Weak transcription	NH-A	brain
13	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
14	chr5:179380200-179389800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:179380200-179401200	Weak transcription	Esophagus	oesophagus
16	chr5:179380400-179389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:179380400-179393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:179381000-179389200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:179381000-179397000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:179381000-179397200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:179381200-179396600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:179381200-179397200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr5:179381200-179402200	Weak transcription	Fetal Heart	heart
25	chr5:179381200-179405600	Weak transcription	NHLF	lung
26	chr5:179381400-179390200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:179381600-179389000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:179381600-179389600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:179381600-179393600	Weak transcription	Osteobl	bone
30	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179381800-179392600	Weak transcription	HSMM	muscle
32	chr5:179381800-179402200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:179382000-179392600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:179382000-179401400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr5:179382200-179389600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:179382200-179401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:179382400-179387400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:179382400-179389200	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:179382600-179387400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr5:179382600-179390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:179382800-179400600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:179383000-179388200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:179383200-179387400	Weak transcription	Brain Anterior Caudate	brain
44	chr5:179383200-179389800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:179383200-179389800	Weak transcription	Ovary	ovary
46	chr5:179383200-179394600	Weak transcription	Stomach Mucosa	stomach
47	chr5:179383200-179408600	Weak transcription	A549	lung
48	chr5:179383400-179388000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:179383400-179388200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:179383400-179388400	Weak transcription	Primary B cells from cord blood	blood

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