Variant report

Variant	rs10875934
Chromosome Location	chr12:49602205-49602206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1039225	0.94[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs10747561	0.94[CHB][hapmap]
rs10747562	0.94[CHB][hapmap]
rs10747563	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10783302	0.94[CHB][hapmap]
rs10783308	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs10875924	0.88[CHB][hapmap]
rs10875928	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs10875931	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs10875935	0.84[CHB][hapmap]
rs11168857	0.94[CHB][hapmap]
rs11168862	0.94[CHB][hapmap]
rs11168884	0.88[CHB][hapmap]
rs11168893	0.90[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap]
rs11168903	0.81[ASN][1000 genomes]
rs11168910	0.94[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap];0.84[YRI][hapmap]
rs11168911	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168912	0.94[ASN][1000 genomes]
rs11168917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168919	1.00[ASN][1000 genomes]
rs11168921	0.83[AFR][1000 genomes]
rs12229524	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs12309994	1.00[ASN][1000 genomes]
rs1874908	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs1991427	0.88[CHB][hapmap]
rs2047101	0.94[CHB][hapmap]
rs2162644	0.94[CHB][hapmap]
rs2279596	0.94[CHB][hapmap]
rs2334930	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs2753	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs3741621	0.94[CHB][hapmap]
rs56149019	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs731350	0.94[CHB][hapmap]
rs7954521	0.88[CHB][hapmap]
rs7954530	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs7957998	0.94[CHB][hapmap]
rs7958241	0.88[CHB][hapmap]
rs7959497	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs7969967	0.94[CHB][hapmap];0.85[CHD][hapmap]
rs9325145	0.94[CHB][hapmap];0.82[CHD][hapmap]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10875934	OR10AD1	cis	cerebellum	SCAN
rs10875934	OR10AD1	cis	parietal	SCAN
rs10875934	RHEBL1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49592800-49608600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:49596000-49608600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:49597400-49606600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:49599000-49602600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:49601400-49602800	Enhancers	Brain Substantia Nigra	brain
6	chr12:49602000-49602600	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr12:49602200-49602800	Enhancers	Brain Cingulate Gyrus	brain
8	chr12:49602200-49603200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links