Variant report

Variant	rs10934892
Chromosome Location	chr3:93864779-93864780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13062355	0.92[MEX][hapmap]
rs13076476	0.84[ASW][hapmap]
rs13099884	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16839759	0.89[EUR][1000 genomes]
rs1902105	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2965	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34309901	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap]
rs34411239	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[GIH][hapmap];0.90[MKK][hapmap]
rs35815512	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap]
rs36010922	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4426680	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4857186	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62266124	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62266156	0.88[EUR][1000 genomes]
rs6764203	0.92[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap]
rs6765621	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6769872	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6777479	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs6791811	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.86[AFR][1000 genomes]
rs7633544	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7637745	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7644769	0.96[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap]
rs7653521	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs9844676	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs9872376	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats 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 target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2755326	chr3:93605126-93882750	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	n/a
8	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10934892	OR5K2	cis	cerebellum	SCAN
rs10934892	ARL6	cis	cerebellum	SCAN
rs10934892	DHFRL1	cis	cerebellum	SCAN
rs10934892	STX19	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:93853000-93864800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:93857800-93865200	Weak transcription	Fetal Brain Female	brain
3	chr3:93863600-93864800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:93864600-93865600	Enhancers	HUES6 Cell Line	embryonic stem cell

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