Variant report

Variant	rs6432593
Chromosome Location	chr2:160965146-160965147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:160955602..160957276-chr2:160963515..160965227,2	MCF-7	breast:
2	chr2:160963372..160965662-chr2:161085963..161088165,2	MCF-7	breast:
3	chr2:160964286..160967312-chr2:161082194..161085973,4	MCF-7	breast:
4	chr2:160964387..160968256-chr2:161077211..161080822,5	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10454740	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]
rs10497208	0.81[CEU][hapmap]
rs10803761	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10929970	0.86[CEU][hapmap]
rs10929971	0.84[CEU][hapmap]
rs11887337	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11897691	0.84[CEU][hapmap]
rs11902965	0.81[CEU][hapmap]
rs12614284	0.81[JPT][hapmap]
rs12692582	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12999707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027372	0.84[CEU][hapmap]
rs13031600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032589	1.00[YRI][hapmap]
rs13394776	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13414434	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13427061	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs1457233	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]
rs1457235	0.83[CEU][hapmap]
rs1457238	0.81[CEU][hapmap]
rs1457240	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1457241	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1471120	0.91[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs1471121	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs16844824	0.81[CEU][hapmap]
rs17341294	0.80[JPT][hapmap]
rs1840893	0.85[EUR][1000 genomes]
rs1902622	0.80[CEU][hapmap]
rs2061288	0.91[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs2357773	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2667031	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2667033	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2715929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2715933	1.00[YRI][hapmap]
rs2925756	0.87[CEU][hapmap];1.00[YRI][hapmap]
rs2925763	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs3792194	0.81[JPT][hapmap]
rs3792196	0.81[JPT][hapmap]
rs4129787	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4233680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4324285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4368286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665149	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4665155	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432582	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6432587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6432600	0.84[CEU][hapmap]
rs6432601	0.84[CEU][hapmap]
rs6432602	0.80[CEU][hapmap]
rs6432603	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720128	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6729540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[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]
rs6749513	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6752593	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6761082	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563574	0.84[CEU][hapmap]
rs7569555	0.81[CEU][hapmap]
rs7579481	0.80[CEU][hapmap]
rs7583743	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7584446	0.80[CEU][hapmap]
rs7598162	0.89[MKK][hapmap]
rs7601113	1.00[YRI][hapmap]
rs7608152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs996112	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6432593	BCR	trans	lymphoblastoid	seeQTL
rs6432593	PLA2R1	cis	cerebellum	SCAN
rs6432593	CYTIP	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160950800-160967000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:160953200-160970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:160954600-160970800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:160954600-160993000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:160954800-160966200	Weak transcription	Fetal Intestine Small	intestine
6	chr2:160955800-160968800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:160956200-160965600	Strong transcription	HMEC	breast
8	chr2:160957000-160970200	Weak transcription	Pancreas	Pancrea
9	chr2:160957400-160981200	Weak transcription	Lung	lung
10	chr2:160958400-160965200	Strong transcription	NHEK	skin
11	chr2:160959200-161004200	Weak transcription	Gastric	stomach
12	chr2:160959400-160985200	Weak transcription	Esophagus	oesophagus
13	chr2:160959400-161032800	Weak transcription	Psoas Muscle	Psoas
14	chr2:160959800-160965800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:160960000-160966400	Weak transcription	HSMMtube	muscle
16	chr2:160960400-160965600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:160961000-160965600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:160962000-160966200	Strong transcription	HSMM	muscle
19	chr2:160962400-160970800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:160962800-160971000	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr2:160963800-160969200	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:160964200-160993600	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:160964400-160965800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:160964400-160967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:160964400-160993600	Weak transcription	Fetal Intestine Large	intestine
26	chr2:160964600-160965400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:160964800-160966200	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr2:160964800-160970800	Weak transcription	Stomach Mucosa	stomach
29	chr2:160965000-160966400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr2:160965000-160968200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links