Variant report

Variant	rs11734196
Chromosome Location	chr4:102796072-102796073
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102792418..102794710-chr4:102794751..102797672,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10212684	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212686	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516482	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097756	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737723	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331846	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641899	1.00[ASN][1000 genomes]
rs12647710	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12647741	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647829	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17031724	0.96[ASN][1000 genomes]
rs1862128	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544569	0.90[ASN][1000 genomes]
rs2631251	0.96[ASN][1000 genomes]
rs2851314	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851315	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851317	0.82[AMR][1000 genomes]
rs2851330	0.90[ASN][1000 genomes]
rs2851331	0.90[ASN][1000 genomes]
rs4317207	0.96[ASN][1000 genomes]
rs4544711	1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4624656	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6812110	0.96[CHD][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6812874	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6849308	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7663733	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666312	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv999861	chr4:102576115-102930562	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2757945	chr4:102662699-103008940	Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759269	chr4:102662699-103008940	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1011180	chr4:102685236-102985945	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537202	chr4:102685236-102985945	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv2757074	chr4:102772861-102933949	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2752360	chr4:102790822-102888822	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11734196	SH2D2A	trans	brain	seeQTL
rs11734196	GUCA1C	trans	brain	seeQTL
rs11734196	ASMT	trans	brain	seeQTL
rs11734196	SLC5A7	trans	brain	seeQTL
rs11734196	ENO3	trans	brain	seeQTL
rs11734196	TTR	trans	brain	seeQTL
rs11734196	LRTM1	trans	brain	seeQTL
rs11734196	CACNA2D4	trans	brain	seeQTL
rs11734196	DEFB119	trans	brain	seeQTL
rs11734196	DAPL1	trans	brain	seeQTL
rs11734196	PDE6H	trans	brain	seeQTL
rs11734196	GSG1	trans	brain	seeQTL
rs11734196	OTX2	trans	brain	seeQTL
rs11734196	CRX	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102787200-102797200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:102792400-102796800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:102792800-102796600	Strong transcription	Primary B cells from cord blood	blood
4	chr4:102794200-102797000	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links