Variant report

Variant	rs2537777
Chromosome Location	chr12:10330098-10330099
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

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	0.82[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs12311169	0.82[AMR][1000 genomes]
rs12822177	0.92[JPT][hapmap]
rs2537778	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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634164	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742110	0.96[MEX][hapmap]
rs2742113	0.92[MEX][hapmap]
rs2742115	0.92[MEX][hapmap]
rs3736232	0.93[JPT][hapmap]
rs3736233	0.93[JPT][hapmap]
rs3736234	0.93[JPT][hapmap]
rs3736235	0.93[JPT][hapmap]
rs3741860	0.88[MEX][hapmap]
rs3816844	0.93[JPT][hapmap]
rs4764299	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6488265	0.96[CEU][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs7296800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7300650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315498	1.00[CEU][hapmap];1.00[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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958778	0.96[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.87[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2537777	EMG1	cis	cerebellum	SCAN
rs2537777	LOH12CR1	cis	cerebellum	SCAN
rs2537777	GRIN2B	cis	cerebellum	SCAN
rs2537777	TPI1	cis	cerebellum	SCAN
rs2537777	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	chr12:10328800-10331400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:10329000-10330200	Enhancers	HMEC	breast
11	chr12:10329000-10331200	Weak transcription	Hela-S3	cervix
12	chr12:10329200-10330200	Enhancers	NHEK	skin
13	chr12:10329600-10331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:10329600-10339000	Weak transcription	Fetal Intestine Large	intestine
15	chr12:10330000-10331200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:10330000-10331600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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