Variant report

Variant	rs4389651
Chromosome Location	chr5:179460968-179460969
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179460277..179462854-chr5:179465782..179468892,3	MCF-7	breast:
2	chr5:179460133..179464010-chr5:179497650..179500177,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1102191	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1103811	0.86[ASN][1000 genomes]
rs12519642	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12654148	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12656814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13161895	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13166286	0.96[AFR][1000 genomes]
rs13179406	0.96[AFR][1000 genomes]
rs17079966	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17079968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248318	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248320	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs27012	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27018	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34027780	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34603792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34674199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35135297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35592104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35608303	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35973843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35988237	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3719	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs379655	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797763	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797764	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs394616	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4129403	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4235504	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438050	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs442181	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs594202	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6873781	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6873994	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6876648	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71613436	0.96[AFR][1000 genomes]
rs71613437	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71613438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs857187	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs857188	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs863231	0.84[ASN][1000 genomes]
rs864481	0.84[ASN][1000 genomes]
rs864482	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:179430600-179462400	Weak transcription	HepG2	liver
9	chr5:179437600-179462600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:179440200-179462600	Weak transcription	Fetal Intestine Large	intestine
12	chr5:179440600-179462400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:179446000-179462200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:179447600-179462400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:179447600-179463200	Weak transcription	Esophagus	oesophagus
16	chr5:179447600-179463200	Weak transcription	Lung	lung
17	chr5:179447600-179463200	Weak transcription	HSMMtube	muscle
18	chr5:179447800-179461600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:179447800-179461600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:179447800-179462400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:179447800-179462400	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:179447800-179463000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:179447800-179463000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:179447800-179463200	Weak transcription	Ovary	ovary
25	chr5:179447800-179466800	Weak transcription	Hela-S3	cervix
26	chr5:179448400-179461400	Weak transcription	Fetal Intestine Small	intestine
27	chr5:179448400-179461600	Weak transcription	Primary B cells from cord blood	blood
28	chr5:179449400-179462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr5:179450600-179466000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:179451000-179462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:179452400-179463400	Weak transcription	Psoas Muscle	Psoas
33	chr5:179454200-179462400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:179454200-179462400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:179454200-179462400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:179454200-179462600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:179454400-179462400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:179454400-179462400	Weak transcription	Fetal Heart	heart
39	chr5:179454600-179461600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:179454600-179461800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:179454600-179462600	Weak transcription	NH-A	brain
42	chr5:179454800-179461400	Weak transcription	Fetal Lung	lung
43	chr5:179454800-179461600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:179454800-179463200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr5:179454800-179464000	Weak transcription	Gastric	stomach
46	chr5:179454800-179464200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:179455000-179461600	Weak transcription	Pancreas	Pancrea
48	chr5:179455000-179462400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr5:179455000-179462400	Weak transcription	Right Ventricle	heart
50	chr5:179455000-179463200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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