Variant report

Variant	rs200944
Chromosome Location	chr10:38150036-38150037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10508861	0.90[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11011371	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1208578	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1208619	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1208621	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12243792	0.90[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12265979	0.90[CEU][hapmap]
rs12412402	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12413083	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12414618	0.84[EUR][1000 genomes]
rs1735625	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17608725	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1779073	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200907	0.92[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200909	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200913	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200914	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200941	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178958	0.83[EUR][1000 genomes]
rs2293962	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2472153	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs2472159	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2472160	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2474545	0.80[EUR][1000 genomes]
rs2474553	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2489166	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2504137	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2738221	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2753883	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739992	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55742761	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59486180	0.83[EUR][1000 genomes]
rs766362	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7895468	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9418311	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs200944	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL
rs200944	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs200944	CUL2	cis	parietal	SCAN
rs200944	ZNF25	cis	parietal	SCAN
rs200944	RP11-162G10.5	cis	Thyroid	GTEx
rs200944	ZNF25	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38148800-38151000	Enhancers	Colon Smooth Muscle	Colon
2	chr10:38149400-38150400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr10:38149400-38150400	Enhancers	Stomach Smooth Muscle	stomach
4	chr10:38149600-38150200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:38149600-38150400	Enhancers	Osteobl	bone
6	chr10:38149600-38150600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:38149800-38151000	Enhancers	Rectal Smooth Muscle	rectum
8	chr10:38150000-38150200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:38150000-38150400	Enhancers	HepG2	liver

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