Variant report

Variant	rs1561267
Chromosome Location	chr2:153492910-153492911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153031040..153034058-chr2:153492264..153495587,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10172024	0.84[YRI][hapmap]
rs10178618	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10185455	0.90[CHD][hapmap];0.80[LWK][hapmap];0.85[ASN][1000 genomes]
rs1036526	0.85[LWK][hapmap];0.95[MKK][hapmap];0.82[YRI][hapmap]
rs11679491	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11883762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052946	0.93[ASN][1000 genomes]
rs13018870	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1370498	0.95[LWK][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs16831451	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs16831529	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16831728	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs16831736	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2272535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293680	0.92[ASN][1000 genomes]
rs2304559	0.80[AFR][1000 genomes]
rs2346534	0.80[AFR][1000 genomes]
rs2346542	0.84[YRI][hapmap]
rs3748941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762507	0.90[LWK][hapmap];0.94[MKK][hapmap];0.84[YRI][hapmap]
rs3811570	0.81[CHD][hapmap]
rs3817620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845678	0.93[ASN][1000 genomes]
rs4146903	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[ASN][1000 genomes]
rs4664119	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664122	0.84[YRI][hapmap]
rs4664600	0.83[AFR][1000 genomes]
rs4664604	0.80[YRI][hapmap]
rs55986999	0.92[ASN][1000 genomes]
rs6434161	0.84[YRI][hapmap]
rs6434162	0.80[YRI][hapmap]
rs6710417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714218	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72858735	0.92[ASN][1000 genomes]
rs72871129	0.85[ASN][1000 genomes]
rs72871192	0.93[ASN][1000 genomes]
rs72872615	0.93[ASN][1000 genomes]
rs746780	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7560393	0.84[YRI][hapmap]
rs7592127	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7604573	0.85[CHD][hapmap]
rs893328	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288125	0.95[LWK][hapmap];0.93[MKK][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv3693437	chr2:153484685-153505003	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153454800-153496600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:153457200-153505000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:153463800-153502800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:153464000-153502800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:153467200-153504000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:153468600-153495800	Weak transcription	Esophagus	oesophagus
7	chr2:153469000-153493800	Weak transcription	Spleen	Spleen
8	chr2:153469000-153496400	Weak transcription	Colonic Mucosa	Colon
9	chr2:153469000-153509800	Weak transcription	Small Intestine	intestine
10	chr2:153469200-153495200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:153469600-153496800	Weak transcription	HSMM	muscle
12	chr2:153471000-153507000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:153472000-153522000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:153473000-153500600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:153473800-153496400	Weak transcription	Osteobl	bone
16	chr2:153474400-153505000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr2:153475800-153493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:153477800-153493800	Weak transcription	HSMMtube	muscle
19	chr2:153477800-153496000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:153477800-153496600	Weak transcription	Aorta	Aorta
21	chr2:153479400-153496200	Weak transcription	NH-A	brain
22	chr2:153481200-153493400	Weak transcription	Fetal Brain Male	brain
23	chr2:153481200-153502200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:153481200-153502400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:153481400-153502400	Strong transcription	Placenta	Placenta
26	chr2:153481400-153503000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:153482000-153493600	Weak transcription	NHLF	lung
28	chr2:153483800-153494400	Weak transcription	NHDF-Ad	bronchial
29	chr2:153484400-153496000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:153484400-153502600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:153484400-153503000	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:153484400-153504200	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:153485200-153494200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:153485200-153500000	Weak transcription	Hela-S3	cervix
35	chr2:153485400-153496800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:153486200-153496600	Weak transcription	HUVEC	blood vessel
37	chr2:153486200-153503000	Strong transcription	Fetal Stomach	stomach
38	chr2:153487600-153505000	Weak transcription	Fetal Thymus	thymus
39	chr2:153488000-153493800	Strong transcription	A549	lung
40	chr2:153488600-153503200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:153488800-153493600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:153489000-153494200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:153489000-153495600	Weak transcription	Right Ventricle	heart
44	chr2:153489000-153496600	Weak transcription	Pancreas	Pancrea
45	chr2:153489200-153493000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:153489200-153495400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr2:153489600-153494200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:153489600-153495000	Weak transcription	Psoas Muscle	Psoas
49	chr2:153489600-153495800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:153489600-153496400	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links