Variant report

Variant	rs2126142
Chromosome Location	chr3:159509442-159509443
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	chr3:159505829..159507763-chr3:159508214..159510388,2	K562	blood:
2	chr3:159506660..159510516-chr3:159511737..159514255,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCHIP1-1	chr3:159509172-159509448	uc_133_+
2	lnc-RP11-432B6.3.1-5	chr3:159509172-159509448	uc_133_-

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11920991	0.91[EUR][1000 genomes]
rs13064339	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13065938	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13066040	0.93[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap]
rs13066560	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13067050	0.82[CEU][hapmap]
rs13075534	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13077427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078322	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs13100094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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]
rs13100614	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs1553080	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16830748	0.85[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs16830780	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076889	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs2366405	0.92[CEU][hapmap]
rs62270390	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6792870	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs7631400	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9860588	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs9880487	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs9884085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:159501800-159510200	Enhancers	Fetal Intestine Large	intestine
3	chr3:159502000-159522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:159503000-159510200	Enhancers	Fetal Intestine Small	intestine
5	chr3:159503800-159509600	Enhancers	Adipose Nuclei	Adipose
6	chr3:159504000-159518600	Enhancers	Brain Hippocampus Middle	brain
7	chr3:159504200-159518400	Enhancers	Brain Substantia Nigra	brain
8	chr3:159504600-159511200	Enhancers	Brain Anterior Caudate	brain
9	chr3:159505000-159515000	Enhancers	Brain Angular Gyrus	brain
10	chr3:159505600-159512600	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:159505600-159515600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:159506000-159518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:159506200-159510000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:159506200-159522600	Weak transcription	Fetal Kidney	kidney
15	chr3:159506400-159511200	Enhancers	A549	lung
16	chr3:159506400-159512400	Weak transcription	Right Atrium	heart
17	chr3:159506400-159512600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:159506400-159513200	Weak transcription	NHLF	lung
19	chr3:159506400-159513800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:159506400-159522400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:159506600-159514200	Weak transcription	Fetal Heart	heart
22	chr3:159506800-159513000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:159507000-159510200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:159507000-159512200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:159507000-159513600	Weak transcription	NH-A	brain
26	chr3:159507400-159512400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:159507400-159512600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:159507600-159509600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:159507600-159510200	Enhancers	Aorta	Aorta
30	chr3:159508000-159513800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:159508000-159513800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:159508000-159514000	Weak transcription	HMEC	breast
33	chr3:159508200-159510600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:159508600-159520600	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:159508800-159509600	Enhancers	Right Ventricle	heart
36	chr3:159508800-159509600	Strong transcription	NHEK	skin
37	chr3:159509000-159510200	Enhancers	HSMM	muscle
38	chr3:159509000-159510400	Enhancers	NHDF-Ad	bronchial
39	chr3:159509000-159510800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:159509000-159516600	Weak transcription	Liver	Liver
41	chr3:159509200-159510200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:159509200-159510200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:159509200-159510200	Enhancers	Left Ventricle	heart
44	chr3:159509200-159515000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:159509200-159516600	Weak transcription	HepG2	liver
46	chr3:159509400-159509600	Genic enhancers	Muscle Satellite Cultured Cells	--
47	chr3:159509400-159509600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:159509400-159509600	Enhancers	Small Intestine	intestine
49	chr3:159509400-159510000	Weak transcription	Esophagus	oesophagus
50	chr3:159509400-159510200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links