Variant report

Variant	rs1457233
Chromosome Location	chr2:160996969-160996970
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	chr2:160992962..160997280-chr2:160998915..161002711,4	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10454740	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10497208	0.80[CEU][hapmap]
rs10803761	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11887337	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11902965	0.80[CEU][hapmap]
rs12692582	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12999707	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031600	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394776	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13414434	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13427061	0.92[CEU][hapmap]
rs1457235	0.83[CEU][hapmap]
rs1457238	0.80[CEU][hapmap]
rs1457240	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1457241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471120	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1471121	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs16844824	0.80[CEU][hapmap]
rs1840893	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061288	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2357773	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2667031	0.83[EUR][1000 genomes]
rs2667033	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2715929	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2925753	0.85[EUR][1000 genomes]
rs2925756	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2925758	0.85[EUR][1000 genomes]
rs2925760	0.84[EUR][1000 genomes]
rs2925763	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs4129787	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233679	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233680	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4324285	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4368286	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4399677	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4665149	0.82[ASN][1000 genomes]
rs4665155	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6432582	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6432587	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6432590	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6432593	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6432603	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720128	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6729540	1.00[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6749513	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6752593	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6761082	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7558852	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569555	0.80[CEU][hapmap]
rs7583743	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608152	0.89[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs897832	0.84[CEU][hapmap]
rs996112	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv459929	chr2:160963603-161079435	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv583497	chr2:160963603-161079435	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875346	chr2:160965335-161044155	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1001502	chr2:160967864-161079450	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1457233	PLA2R1	cis	cerebellum	SCAN
rs1457233	CYTIP	cis	cerebellum	SCAN
rs1457233	BCR	trans	lymphoblastoid	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160959200-161004200	Weak transcription	Gastric	stomach
2	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
3	chr2:160983200-161005200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:160990000-161005000	Weak transcription	Colonic Mucosa	Colon
5	chr2:160993200-161002200	Weak transcription	Lung	lung
6	chr2:160993600-160998600	Strong transcription	HMEC	breast
7	chr2:160993600-160998800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:160993800-160997200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:160994000-160997200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:160994200-160998400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:160994400-160998600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:160994400-160999000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:160994400-161002000	Weak transcription	Esophagus	oesophagus
14	chr2:160994400-161002000	Weak transcription	Fetal Intestine Large	intestine
15	chr2:160994400-161004200	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:160994400-161014800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:160994400-161037400	Weak transcription	Pancreas	Pancrea
18	chr2:160994600-161038000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr2:160994800-160998000	Weak transcription	NHEK	skin
20	chr2:160994800-160998600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:160994800-161001000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:160994800-161002000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:160995000-160999000	Genic enhancers	HSMM	muscle
24	chr2:160995600-160997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:160996200-160999200	Enhancers	Osteobl	bone
26	chr2:160996400-160997000	Enhancers	Rectal Smooth Muscle	rectum
27	chr2:160996400-160997400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:160996400-160997600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:160996400-160997800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:160996400-160998600	Enhancers	NHDF-Ad	bronchial
31	chr2:160996400-160999000	Enhancers	HSMMtube	muscle
32	chr2:160996600-160997200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr2:160996800-160997000	Enhancers	Fetal Stomach	stomach
34	chr2:160996800-160997000	Enhancers	Stomach Mucosa	stomach
35	chr2:160996800-160997200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:160996800-160997200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:160996800-160997200	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:160996800-160997200	Enhancers	Fetal Intestine Small	intestine
39	chr2:160996800-160997200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:160996800-160997200	Enhancers	A549	lung
41	chr2:160996800-160997200	Flanking Active TSS	NHLF	lung
42	chr2:160996800-160997400	Enhancers	Fetal Lung	lung
43	chr2:160996800-160997600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:160996800-160999000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links