Variant report

Variant	rs16856086
Chromosome Location	chr1:180493944-180493945
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	chr1:180491568..180494207-chr1:180499661..180501962,2	MCF-7	breast:
2	chr1:180491722..180497520-chr1:180497939..180503107,7	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10753211	0.81[CHB][hapmap]
rs10753216	0.82[ASN][1000 genomes]
rs10798759	0.81[CHB][hapmap]
rs10798762	0.81[CHB][hapmap]
rs10913969	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10913980	0.81[CHB][hapmap]
rs10913981	0.81[CHB][hapmap]
rs10913984	0.81[CHB][hapmap]
rs10913985	0.81[CHB][hapmap]
rs10913994	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10914007	0.82[JPT][hapmap]
rs10914018	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs10914023	0.80[CHD][hapmap]
rs11580793	0.81[CHB][hapmap]
rs12034217	0.81[CHB][hapmap]
rs12039331	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12039933	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12041620	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091722	0.90[CHB][hapmap]
rs12404209	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12405902	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12565492	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs12730889	0.81[CHB][hapmap]
rs1341924	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs1416823	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs1538620	0.81[CHB][hapmap]
rs16856087	0.96[ASN][1000 genomes]
rs1890731	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1970400	0.88[EUR][1000 genomes]
rs2877415	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs3737584	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs3806300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3806301	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs4076403	0.81[CHB][hapmap]
rs4421553	0.81[CHB][hapmap]
rs4543756	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4578179	0.80[CHB][hapmap]
rs4642852	0.81[JPT][hapmap]
rs4651064	0.81[CHB][hapmap]
rs4652505	0.80[CHB][hapmap]
rs6425634	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs6425641	0.87[EUR][1000 genomes]
rs6425644	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425645	0.94[ASN][1000 genomes]
rs6670544	0.81[CHB][hapmap]
rs6687442	0.88[EUR][1000 genomes]
rs6687549	0.88[EUR][1000 genomes]
rs6699076	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6699585	0.88[EUR][1000 genomes]
rs6704334	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs6704437	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs72720915	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72720917	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72720922	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521151	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7528650	0.81[CHB][hapmap]
rs7532806	0.82[CHB][hapmap]
rs9701037	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9726041	0.90[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes]
rs9730180	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes]

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:41 , 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	chr1:180491400-180494000	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:180491400-180496200	Weak transcription	A549	lung
9	chr1:180491400-180496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:180491400-180499400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:180491600-180511200	Weak transcription	Psoas Muscle	Psoas
12	chr1:180492000-180494000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:180492000-180494000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:180492000-180494800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:180492000-180495400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:180492000-180495400	Weak transcription	K562	blood
17	chr1:180492200-180494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:180492200-180494000	Weak transcription	Fetal Heart	heart
19	chr1:180492200-180494600	Weak transcription	Fetal Intestine Small	intestine
20	chr1:180492200-180494800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:180492200-180495800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:180492400-180496400	Weak transcription	NHEK	skin
23	chr1:180492400-180499400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:180492400-180503000	Weak transcription	Pancreas	Pancrea
25	chr1:180492600-180495400	Weak transcription	HepG2	liver
26	chr1:180492600-180498000	Weak transcription	HSMMtube	muscle
27	chr1:180493000-180496200	Weak transcription	Hela-S3	cervix
28	chr1:180493200-180494600	Enhancers	HMEC	breast
29	chr1:180493200-180495000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:180493400-180494400	Enhancers	Right Ventricle	heart
31	chr1:180493400-180494600	Enhancers	Left Ventricle	heart
32	chr1:180493400-180495000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr1:180493400-180496600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:180493600-180494000	Weak transcription	Fetal Stomach	stomach
35	chr1:180493800-180494000	Enhancers	Fetal Lung	lung
36	chr1:180493800-180494200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:180493800-180495000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:180493800-180495000	Enhancers	Lung	lung
39	chr1:180493800-180495000	Enhancers	Right Atrium	heart
40	chr1:180493800-180495400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:180493800-180497000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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