Variant report

Variant	rs11858440
Chromosome Location	chr15:53926729-53926730
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	chr15:53926573..53928626-chr15:53929111..53931457,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10851542	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10851543	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857733	0.86[ASN][1000 genomes]
rs11858504	0.86[ASN][1000 genomes]
rs17549560	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1878184	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1906397	0.85[ASN][1000 genomes]
rs1906400	0.89[ASN][1000 genomes]
rs1906402	0.92[ASN][1000 genomes]
rs1906403	0.92[ASN][1000 genomes]
rs1906404	0.92[ASN][1000 genomes]
rs1906410	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1906433	0.81[CHB][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap]
rs1906439	0.86[ASN][1000 genomes]
rs2414248	0.86[ASN][1000 genomes]
rs2414249	0.86[ASN][1000 genomes]
rs2414254	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2899518	0.84[ASN][1000 genomes]
rs34753685	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35292476	0.92[ASN][1000 genomes]
rs35487869	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3911726	0.86[ASN][1000 genomes]
rs4332691	0.86[ASN][1000 genomes]
rs4387549	0.88[ASN][1000 genomes]
rs4643263	0.86[ASN][1000 genomes]
rs62005937	0.92[ASN][1000 genomes]
rs62005939	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62005944	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67494345	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs690545	0.85[ASN][1000 genomes]
rs7172766	0.92[ASN][1000 genomes]
rs7183565	0.88[ASN][1000 genomes]
rs72747328	0.88[ASN][1000 genomes]
rs72747347	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7495833	0.92[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv833009	chr15:53752901-53935303	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv9267	chr15:53821005-54132612	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv569435	chr15:53845097-53966805	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv934282	chr15:53872148-53989432	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv527474	chr15:53874591-53991833	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1043995	chr15:53907679-53968209	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11858440	KIAA1370	cis	parietal	SCAN
rs11858440	UNC13C	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53925000-53926800	Weak transcription	Pancreas	Pancrea
2	chr15:53925000-53927000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:53925600-53926800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:53925600-53926800	Weak transcription	Liver	Liver
5	chr15:53926400-53927600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links