Variant report

Variant	rs16856087
Chromosome Location	chr1:180494140-180494141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180491568..180494207-chr1:180499661..180501962,2	MCF-7	breast:
2	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:
3	chr1:180494034..180495925-chr1:180548786..180551301,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10737342	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10798761	0.86[JPT][hapmap]
rs10798767	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs10913969	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.82[EUR][1000 genomes]
rs10913970	0.82[EUR][1000 genomes]
rs10913994	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10914002	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs10914007	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes]
rs10914018	0.81[CHB][hapmap]
rs12024156	0.90[EUR][1000 genomes]
rs12034669	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12039331	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12039933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12041620	0.96[ASN][1000 genomes]
rs12045123	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12085808	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12091722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs12402815	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12403665	0.85[EUR][1000 genomes]
rs12404209	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12405902	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.82[EUR][1000 genomes]
rs12407122	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12565492	0.81[CHB][hapmap]
rs12691484	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs1341924	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs1416823	0.95[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs1418102	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs16856086	0.96[ASN][1000 genomes]
rs1890731	0.81[ASN][1000 genomes]
rs28506072	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2877415	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.85[EUR][1000 genomes]
rs3737584	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3806300	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4483365	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4543756	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4642852	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4652496	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4652498	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4652499	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs60286873	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425625	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs6425634	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6425644	0.81[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6425645	0.90[ASN][1000 genomes]
rs6661208	0.85[JPT][hapmap]
rs6680368	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs6699076	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6704334	0.83[CHB][hapmap]
rs6704437	0.84[CHB][hapmap]
rs72720922	0.96[ASN][1000 genomes]
rs7519288	1.00[CEU][hapmap]
rs7526189	0.82[EUR][1000 genomes]
rs7539910	0.85[CHB][hapmap]
rs7541993	0.80[CHB][hapmap]
rs7552084	0.84[CHB][hapmap]
rs822706	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs9726041	0.84[CHB][hapmap]
rs9730180	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180486000-180499400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:180488000-180500400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:180488600-180497000	Enhancers	Placenta	Placenta
4	chr1:180489400-180494400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:180489800-180494400	Weak transcription	HUVEC	blood vessel
6	chr1:180491000-180499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:180491400-180496200	Weak transcription	A549	lung
8	chr1:180491400-180496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
11	chr1:180492000-180494800	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:180492000-180495400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:180492000-180495400	Weak transcription	K562	blood
14	chr1:180492200-180494600	Weak transcription	Fetal Intestine Small	intestine
15	chr1:180492200-180494800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:180492200-180495800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:180492400-180496400	Weak transcription	NHEK	skin
18	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
20	chr1:180492600-180495400	Weak transcription	HepG2	liver
21	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle
22	chr1:180493000-180496200	Weak transcription	Hela-S3	cervix
23	chr1:180493200-180494600	Enhancers	HMEC	breast
24	chr1:180493200-180495000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:180493400-180494400	Enhancers	Right Ventricle	heart
26	chr1:180493400-180494600	Enhancers	Left Ventricle	heart
27	chr1:180493400-180495000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:180493400-180496600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:180493800-180494200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:180493800-180495000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:180493800-180495000	Enhancers	Lung	lung
32	chr1:180493800-180495000	Enhancers	Right Atrium	heart
33	chr1:180493800-180495400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:180493800-180497000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:180494000-180494200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr1:180494000-180494200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:180494000-180494400	Weak transcription	Fetal Lung	lung
38	chr1:180494000-180494600	Enhancers	Fetal Heart	heart
39	chr1:180494000-180494600	Enhancers	Fetal Muscle Leg	muscle
40	chr1:180494000-180495000	Enhancers	Esophagus	oesophagus
41	chr1:180494000-180495000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr1:180494000-180495200	Enhancers	Fetal Stomach	stomach
43	chr1:180494000-180495400	Enhancers	Aorta	Aorta
44	chr1:180494000-180496800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr1:180494000-180497200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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