Variant report

Variant	rs7629154
Chromosome Location	chr3:160520555-160520556
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	chr3:160513259..160516252-chr3:160518883..160520924,2	MCF-7	breast:
2	chr3:160518067..160520836-chr3:160522097..160523990,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1159747	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs1378662	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs1378663	1.00[CEU][hapmap]
rs1455870	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1455871	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs16831442	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16831457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831470	0.86[YRI][hapmap]
rs16831471	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831516	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs16831520	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17236620	0.94[EUR][1000 genomes]
rs17236641	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17236648	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236655	1.00[EUR][1000 genomes]
rs17236662	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17826352	0.94[EUR][1000 genomes]
rs17826358	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs17826364	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17826370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947498	0.86[CHB][hapmap]
rs2068817	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs34035435	0.97[EUR][1000 genomes]
rs3907061	0.94[EUR][1000 genomes]
rs4549318	0.97[EUR][1000 genomes]
rs4627794	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes]
rs55891037	1.00[EUR][1000 genomes]
rs55905728	1.00[EUR][1000 genomes]
rs55923270	0.94[EUR][1000 genomes]
rs55997050	1.00[EUR][1000 genomes]
rs56083575	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56141155	1.00[EUR][1000 genomes]
rs56157815	1.00[EUR][1000 genomes]
rs56180903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56221606	0.81[AFR][1000 genomes]
rs56331465	1.00[EUR][1000 genomes]
rs57828617	0.94[EUR][1000 genomes]
rs58891820	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59264052	0.81[AFR][1000 genomes]
rs60447858	0.81[AFR][1000 genomes]
rs6768524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6771910	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[EUR][1000 genomes]
rs6779461	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73877951	0.81[AFR][1000 genomes]
rs73877952	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73877961	0.81[AFR][1000 genomes]
rs73877966	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73877967	0.81[AFR][1000 genomes]
rs7618082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618596	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633370	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7633401	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7639930	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs9837945	0.87[CEU][hapmap];0.93[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160498400-160522600	Weak transcription	Right Ventricle	heart
2	chr3:160509000-160522600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:160513400-160522600	Weak transcription	Pancreas	Pancrea
4	chr3:160514400-160522600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:160515400-160526400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:160518800-160522800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:160519000-160521000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:160519200-160521000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr3:160519200-160521000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:160519200-160521000	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr3:160519600-160521000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:160519600-160522400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:160519800-160521000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:160520000-160520800	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:160520000-160521000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:160520000-160521000	Enhancers	Psoas Muscle	Psoas
17	chr3:160520000-160521000	Enhancers	Right Atrium	heart
18	chr3:160520200-160520600	Enhancers	Adipose Nuclei	Adipose
19	chr3:160520200-160520800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:160520200-160521000	Enhancers	Primary T cells from cord blood	blood
21	chr3:160520200-160521000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:160520200-160521000	Enhancers	Colon Smooth Muscle	Colon
23	chr3:160520200-160521000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr3:160520200-160521200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:160520200-160522600	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:160520200-160522600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:160520200-160522600	Weak transcription	Fetal Brain Female	brain
28	chr3:160520200-160525800	Weak transcription	Liver	Liver
29	chr3:160520200-160526000	Weak transcription	Aorta	Aorta
30	chr3:160520200-160526000	Weak transcription	Brain Angular Gyrus	brain
31	chr3:160520200-160526400	Weak transcription	Stomach Mucosa	stomach
32	chr3:160520400-160520800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:160520400-160520800	Weak transcription	Placenta	Placenta
34	chr3:160520400-160521000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:160520400-160521000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:160520400-160521000	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:160520400-160522000	Weak transcription	Fetal Heart	heart
38	chr3:160520400-160522400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:160520400-160522400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:160520400-160522600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:160520400-160522600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:160520400-160522600	Weak transcription	Gastric	stomach
43	chr3:160520400-160522600	Weak transcription	Left Ventricle	heart
44	chr3:160520400-160522600	Weak transcription	Lung	lung
45	chr3:160520400-160522600	Weak transcription	NHDF-Ad	bronchial
46	chr3:160520400-160526400	Weak transcription	Brain Anterior Caudate	brain
47	chr3:160520400-160529600	Weak transcription	Colonic Mucosa	Colon

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