Variant report

Variant	rs11856538
Chromosome Location	chr15:77383211-77383212
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77376000..77380295-chr15:77383210..77388608,6	MCF-7	breast:
2	chr15:77377099..77380194-chr15:77383029..77386419,3	K562	blood:

Variant related genes	Relation type
ENSG00000140391	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10519158	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11853625	0.83[ASN][1000 genomes]
rs11853633	0.90[ASN][1000 genomes]
rs11854182	0.90[ASN][1000 genomes]
rs11856513	0.96[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11857330	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs12324366	0.88[JPT][hapmap]
rs12900110	0.81[EUR][1000 genomes]
rs12902106	0.82[EUR][1000 genomes]
rs12902434	0.81[EUR][1000 genomes]
rs12902446	0.92[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13379686	0.92[ASN][1000 genomes]
rs13380152	0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs1374201	0.93[CHD][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.88[ASN][1000 genomes]
rs1446313	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs16968730	0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs17381652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17381821	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs17383078	0.87[ASN][1000 genomes]
rs17466480	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867780	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs2044453	0.96[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2292594	0.96[CHD][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.83[ASN][1000 genomes]
rs34572155	0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs35093280	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4592615	0.96[CEU][hapmap];0.88[JPT][hapmap]
rs4638539	0.88[ASN][1000 genomes]
rs4886514	0.81[EUR][1000 genomes]
rs4886852	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs55881066	0.83[ASN][1000 genomes]
rs59831220	0.90[ASN][1000 genomes]
rs60863150	0.83[ASN][1000 genomes]
rs7173670	0.90[ASN][1000 genomes]
rs74025074	0.92[ASN][1000 genomes]
rs74027548	0.83[ASN][1000 genomes]
rs74027549	0.81[ASN][1000 genomes]
rs7496431	0.96[CHD][hapmap];0.87[JPT][hapmap];0.90[LWK][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv904414	chr15:77304310-77400388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11856538	CYP1A2	cis	cerebellum	SCAN
rs11856538	HMG20A	cis	parietal	SCAN
rs11856538	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77376800-77395600	Weak transcription	Fetal Intestine Small	intestine
2	chr15:77378600-77392000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:77380000-77389200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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