Variant report

Variant	rs10078977
Chromosome Location	chr5:179458527-179458528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179448841..179450678-chr5:179458129..179460893,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10036834	0.81[CEU][hapmap]
rs10045755	0.81[ASN][1000 genomes]
rs10061480	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10068039	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10068529	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10068594	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10479455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479557	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10903246	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1102190	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12153541	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12653944	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12656219	0.81[CHB][hapmap]
rs173562	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs185076	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193718	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs248257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs248258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs248316	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248319	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[EUR][1000 genomes]
rs27014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27016	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs27017	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs27019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35928331	0.88[ASN][1000 genomes]
rs394588	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4130025	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs418384	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4340879	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4466125	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs449511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4700855	0.81[CHB][hapmap]
rs55734821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405020	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62405021	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6871596	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6884290	0.81[ASN][1000 genomes]
rs6888883	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7706570	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs857181	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs857182	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs857183	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs857189	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9329096	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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:94 , 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	chr5:179447600-179459600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr5:179447600-179462400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr5:179447600-179463200	Weak transcription	Esophagus	oesophagus
17	chr5:179447600-179463200	Weak transcription	Lung	lung
18	chr5:179447600-179463200	Weak transcription	HSMMtube	muscle
19	chr5:179447800-179461600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:179447800-179461600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:179447800-179462400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:179447800-179462400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:179447800-179463000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:179447800-179463000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:179447800-179463200	Weak transcription	Ovary	ovary
26	chr5:179447800-179466800	Weak transcription	Hela-S3	cervix
27	chr5:179448000-179458600	Weak transcription	A549	lung
28	chr5:179448200-179459400	Weak transcription	Fetal Stomach	stomach
29	chr5:179448400-179461400	Weak transcription	Fetal Intestine Small	intestine
30	chr5:179448400-179461600	Weak transcription	Primary B cells from cord blood	blood
31	chr5:179449000-179459400	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:179449000-179460200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:179449400-179462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:179450600-179466000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr5:179451000-179462600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:179451200-179460400	Weak transcription	Liver	Liver
37	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:179452200-179459400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:179452400-179463400	Weak transcription	Psoas Muscle	Psoas
40	chr5:179454000-179459200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:179454200-179462400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:179454200-179462400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:179454200-179462400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:179454200-179462600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:179454400-179462400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:179454400-179462400	Weak transcription	Fetal Heart	heart
47	chr5:179454600-179459000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:179454600-179461600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:179454600-179461800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr5:179454600-179462600	Weak transcription	NH-A	brain

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