Variant report

Variant	rs4964352
Chromosome Location	chr12:105673262-105673263
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105672889..105673823-chr12:105777116..105777625,2	MCF-7	breast:
2	chr12:105669318..105671725-chr12:105671991..105674954,2	K562	blood:
3	chr12:105673064..105673821-chr12:105772193..105773537,4	MCF-7	breast:
4	chr12:105672864..105673858-chr12:105772686..105773396,2	MCF-7	breast:
5	chr12:105670361..105673548-chr12:105673621..105675351,3	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1014502	0.84[CEU][hapmap]
rs10459165	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10778377	0.93[ASN][1000 genomes]
rs10778378	0.93[ASN][1000 genomes]
rs10778379	0.93[ASN][1000 genomes]
rs10861359	0.84[CEU][hapmap]
rs10861361	0.84[CEU][hapmap]
rs10861363	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10861367	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10861370	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861372	0.93[ASN][1000 genomes]
rs10861373	0.93[ASN][1000 genomes]
rs10861374	0.93[ASN][1000 genomes]
rs10861375	0.92[ASN][1000 genomes]
rs10861376	0.93[ASN][1000 genomes]
rs10861379	0.93[ASN][1000 genomes]
rs10861380	0.91[ASN][1000 genomes]
rs11112370	0.84[CEU][hapmap]
rs11112376	0.84[CEU][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap]
rs11112412	0.84[CEU][hapmap]
rs11112416	0.84[CEU][hapmap]
rs11112421	0.87[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.82[AFR][1000 genomes]
rs11112423	0.82[AFR][1000 genomes]
rs11112432	0.87[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.82[AFR][1000 genomes]
rs11112433	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11112440	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112442	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112443	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112444	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11112446	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112447	0.93[ASN][1000 genomes]
rs11112449	0.93[ASN][1000 genomes]
rs11112450	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11831854	0.84[CEU][hapmap]
rs12227922	0.91[ASN][1000 genomes]
rs12228258	0.93[ASN][1000 genomes]
rs12424651	0.91[ASN][1000 genomes]
rs12578428	0.93[ASN][1000 genomes]
rs12578730	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579536	0.84[ASN][1000 genomes]
rs12579816	0.93[ASN][1000 genomes]
rs12580027	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12582119	0.93[ASN][1000 genomes]
rs12582382	0.93[ASN][1000 genomes]
rs12582412	0.93[ASN][1000 genomes]
rs12815031	0.83[CEU][hapmap]
rs12819795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1317955	0.84[CEU][hapmap];0.89[GIH][hapmap]
rs1373552	0.84[CEU][hapmap]
rs1444611	0.83[CEU][hapmap]
rs1897482	0.81[ASN][1000 genomes]
rs2272495	0.84[CEU][hapmap];0.90[LWK][hapmap]
rs2293643	0.87[ASW][hapmap];0.84[CEU][hapmap];0.90[LWK][hapmap];0.96[MKK][hapmap]
rs2293644	0.84[CEU][hapmap]
rs34983773	0.82[AFR][1000 genomes]
rs3794223	0.88[CEU][hapmap]
rs3794227	0.89[GIH][hapmap]
rs3817607	0.87[ASW][hapmap];0.84[CEU][hapmap];0.90[LWK][hapmap];0.86[MKK][hapmap]
rs4337137	0.95[ASN][1000 genomes]
rs4578495	0.91[ASN][1000 genomes]
rs4964129	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964336	0.83[CEU][hapmap]
rs4964347	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964349	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964351	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4964353	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4964354	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132894	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132958	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7295178	0.93[ASN][1000 genomes]
rs7299570	0.91[ASN][1000 genomes]
rs7300350	0.93[ASN][1000 genomes]
rs7308679	0.93[ASN][1000 genomes]
rs73181849	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484699	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7485511	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7485535	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7487098	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs755604	0.84[CEU][hapmap]
rs881279	0.84[CEU][hapmap];0.89[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1044450	chr12:105668451-105682822	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4964352	APPL2	cis	cerebellum	SCAN
rs4964352	C12orf75	cis	cerebellum	SCAN
rs4964352	TDG	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105665000-105674200	Weak transcription	Osteobl	bone
2	chr12:105665600-105674800	Weak transcription	NHDF-Ad	bronchial
3	chr12:105668200-105674800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:105668600-105673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:105670400-105674600	Weak transcription	NHEK	skin
6	chr12:105670400-105674800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:105670600-105675000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:105670600-105675000	Weak transcription	HMEC	breast
9	chr12:105671400-105673800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr12:105672400-105673400	Weak transcription	Gastric	stomach
11	chr12:105672400-105673400	Weak transcription	Pancreas	Pancrea
12	chr12:105672400-105673400	Weak transcription	NHLF	lung
13	chr12:105672800-105674200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:105673000-105674000	Enhancers	A549	lung
15	chr12:105673200-105674000	Weak transcription	Fetal Intestine Large	intestine
16	chr12:105673200-105675800	Enhancers	Stomach Mucosa	stomach
17	chr12:105673200-105676200	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links