Variant report

Variant	rs12371662
Chromosome Location	chr12:66661529-66661530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66630936..66633902-chr12:66659450..66661636,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10748037	0.96[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs10784519	0.96[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10784520	0.84[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10878396	0.96[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs10878397	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11176115	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11176117	0.90[EUR][1000 genomes]
rs11176120	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610967	0.82[CHB][hapmap]
rs1168324	0.93[EUR][1000 genomes]
rs12146776	0.86[EUR][1000 genomes]
rs12423377	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12818303	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12822967	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1603244	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1816562	0.96[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs2047236	0.87[EUR][1000 genomes]
rs2047237	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088169	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2118137	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs289065	0.96[EUR][1000 genomes]
rs6581669	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7137005	0.96[EUR][1000 genomes]
rs7137378	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7138034	0.88[EUR][1000 genomes]
rs724739	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724742	0.88[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7315361	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7959802	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs7972934	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9971666	0.91[EUR][1000 genomes]

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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12371662	HELB	cis	parietal	SCAN
rs12371662	HELB	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66646000-66662000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr12:66650800-66663400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:66658200-66663600	Weak transcription	Thymus	Thymus
4	chr12:66660200-66662000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:66660600-66662000	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr12:66660800-66662200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:66660800-66663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:66660800-66663800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr12:66661000-66664800	Enhancers	Primary T cells from cord blood	blood
10	chr12:66661200-66661600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr12:66661200-66663600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:66661200-66663600	Enhancers	GM12878-XiMat	blood
13	chr12:66661200-66664600	Enhancers	Primary B cells from cord blood	blood
14	chr12:66661200-66666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:66661400-66661600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:66661400-66661600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:66661400-66661600	Enhancers	Brain Hippocampus Middle	brain
18	chr12:66661400-66661800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:66661400-66663000	Enhancers	NHEK	skin

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