Variant report

Variant	rs11596697
Chromosome Location	chr10:97671022-97671023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97666246..97669284-chr10:97669704..97672304,3	MCF-7	breast:
2	chr10:97666965..97669920-chr10:97670050..97671607,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BLNK-6	chr10:97668685-97671344	ucscGeneNc_uc001klj_1

Variant related genes	Relation type
ENSG00000173088	Chromatin interaction
ENSG00000226688	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11592937	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11594010	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11594340	0.88[AFR][1000 genomes]
rs11594853	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11595122	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11597564	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11599779	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12761082	0.80[AMR][1000 genomes]
rs12761960	1.00[YRI][hapmap]
rs12767650	1.00[YRI][hapmap]
rs12770313	1.00[YRI][hapmap]
rs12770849	1.00[YRI][hapmap]
rs12775584	1.00[CHD][hapmap]
rs3176886	1.00[YRI][hapmap]
rs3176888	1.00[YRI][hapmap]
rs3181115	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34630379	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34833309	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34955155	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34963139	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35298116	0.80[AMR][1000 genomes]
rs35691144	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35700869	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs35864527	0.80[AMR][1000 genomes]
rs35968758	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36103691	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66527979	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66530311	0.80[AMR][1000 genomes]
rs66706740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66751616	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67166869	0.80[AMR][1000 genomes]
rs68078796	0.88[AFR][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	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
2	nsv895905	chr10:97513362-97686064	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv895906	chr10:97513362-97703650	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv895907	chr10:97529318-97686064	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
5	nsv895908	chr10:97544513-97724247	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11596697	C10orf12	cis	cerebellum	SCAN
rs11596697	PIPSL	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97668200-97693600	Weak transcription	Fetal Stomach	stomach
2	chr10:97668400-97673600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links