Variant report

Variant	rs7949316
Chromosome Location	chr11:120495204-120495205
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10790388	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10892588	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs11600274	0.82[ASN][1000 genomes]
rs11601552	0.95[ASN][1000 genomes]
rs11602011	0.92[ASN][1000 genomes]
rs11603831	1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs11604139	0.89[ASN][1000 genomes]
rs11605735	0.94[ASN][1000 genomes]
rs12278532	0.94[ASN][1000 genomes]
rs12807172	0.81[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1320721	0.80[EUR][1000 genomes]
rs34759019	0.95[ASN][1000 genomes]
rs34884722	0.94[ASN][1000 genomes]
rs4245039	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4331108	0.87[ASN][1000 genomes]
rs4367952	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4414229	0.87[EUR][1000 genomes]
rs4445643	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4565903	0.81[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4611216	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4936525	0.81[EUR][1000 genomes]
rs4936526	0.81[EUR][1000 genomes]
rs4936529	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6589819	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6589820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6589821	0.91[ASN][1000 genomes]
rs7101412	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111020	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7127199	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924856	0.82[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7928043	0.87[ASN][1000 genomes]
rs7934084	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947677	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7952478	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1036102	chr11:120442895-120498908	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv468881	chr11:120446830-120551100	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv556476	chr11:120446830-120551100	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7949316	C11orf63	cis	parietal	SCAN
rs7949316	HSPA8	cis	parietal	SCAN
rs7949316	BCL9L	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120484800-120507400	Weak transcription	Right Atrium	heart
2	chr11:120485400-120498200	Weak transcription	Ovary	ovary
3	chr11:120489600-120500200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:120489800-120499600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:120490000-120500200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:120491200-120498000	Weak transcription	Fetal Intestine Small	intestine
7	chr11:120493800-120497600	Weak transcription	Fetal Intestine Large	intestine
8	chr11:120493800-120500200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:120493800-120500200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:120494000-120504600	Weak transcription	Fetal Lung	lung
11	chr11:120494800-120498000	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links