Variant report

Variant	rs3797769
Chromosome Location	chr5:179388586-179388587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179387216..179389943-chr5:179396226..179399664,3	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17079774	1.00[CEU][hapmap]
rs2162760	0.92[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3797772	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs61742526	1.00[AFR][1000 genomes];0.87[AMR][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:106 , 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	chr5:179375400-179392600	Weak transcription	Fetal Kidney	kidney
6	chr5:179376600-179389800	Weak transcription	Placenta	Placenta
7	chr5:179376600-179390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
9	chr5:179379000-179389800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr5:179379000-179390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:179380000-179392600	Weak transcription	NH-A	brain
12	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
13	chr5:179380200-179389800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:179380200-179401200	Weak transcription	Esophagus	oesophagus
15	chr5:179380400-179389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:179380400-179393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:179381000-179389200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:179381000-179397000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:179381000-179397200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:179381200-179396600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:179381200-179397200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr5:179381200-179402200	Weak transcription	Fetal Heart	heart
24	chr5:179381200-179405600	Weak transcription	NHLF	lung
25	chr5:179381400-179390200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:179381600-179389000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:179381600-179389600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:179381600-179393600	Weak transcription	Osteobl	bone
29	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179381800-179392600	Weak transcription	HSMM	muscle
31	chr5:179381800-179402200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:179382000-179392600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr5:179382000-179401400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:179382200-179389600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:179382200-179401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:179382400-179389200	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:179382600-179390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:179382800-179400600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:179383200-179389800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179383200-179389800	Weak transcription	Ovary	ovary
41	chr5:179383200-179394600	Weak transcription	Stomach Mucosa	stomach
42	chr5:179383200-179408600	Weak transcription	A549	lung
43	chr5:179383400-179388600	Weak transcription	Right Ventricle	heart
44	chr5:179383400-179388800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:179383400-179389800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:179383800-179388800	Weak transcription	Aorta	Aorta
47	chr5:179383800-179388800	Weak transcription	Lung	lung
48	chr5:179383800-179388800	Weak transcription	Spleen	Spleen
49	chr5:179383800-179389000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:179383800-179389000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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