Variant report

Variant	rs2537778
Chromosome Location	chr12:10329817-10329818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1050283	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs1050286	0.85[JPT][hapmap]
rs10505755	0.93[JPT][hapmap]
rs11053647	0.90[JPT][hapmap]
rs11053648	0.93[JPT][hapmap]
rs11053649	0.92[JPT][hapmap]
rs11053654	0.81[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs12822177	0.92[JPT][hapmap]
rs2537777	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537779	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634164	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742110	0.91[MEX][hapmap]
rs2742113	0.96[MEX][hapmap]
rs2742115	0.91[MEX][hapmap]
rs3736232	0.93[JPT][hapmap]
rs3736233	0.93[JPT][hapmap]
rs3736234	0.93[JPT][hapmap]
rs3736235	0.93[JPT][hapmap]
rs3741860	0.96[MEX][hapmap]
rs3816844	0.93[JPT][hapmap]
rs4764299	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6488265	0.96[CEU][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7296800	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300650	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305138	0.84[MEX][hapmap]
rs7315498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958778	0.88[ASW][hapmap];0.96[CEU][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2537778	EMG1	cis	cerebellum	SCAN
rs2537778	TPI1	cis	cerebellum	SCAN
rs2537778	LOH12CR1	cis	cerebellum	SCAN
rs2537778	GNB3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10321800-10331200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:10325400-10330600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:10325400-10330600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:10325400-10335000	Weak transcription	A549	lung
5	chr12:10326200-10334800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:10327600-10330200	Enhancers	Fetal Intestine Small	intestine
7	chr12:10327800-10330200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:10328600-10330600	Weak transcription	Placenta	Placenta
9	chr12:10328800-10330000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:10328800-10331400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:10329000-10330000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:10329000-10330200	Enhancers	HMEC	breast
13	chr12:10329000-10331200	Weak transcription	Hela-S3	cervix
14	chr12:10329200-10330200	Enhancers	NHEK	skin
15	chr12:10329600-10331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:10329600-10339000	Weak transcription	Fetal Intestine Large	intestine

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