Variant report

Variant	rs11161831
Chromosome Location	chr1:86904993-86904994
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493790	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs10873785	0.88[ASN][1000 genomes]
rs11161812	0.88[CEU][hapmap]
rs11161814	0.81[CHB][hapmap]
rs11161816	0.88[CEU][hapmap]
rs11161817	0.81[AMR][1000 genomes]
rs1158833	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs1182098	0.83[CEU][hapmap]
rs1182099	0.84[CEU][hapmap]
rs12145243	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs12146009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403033	0.87[CEU][hapmap]
rs12406320	0.82[CEU][hapmap];0.81[AMR][1000 genomes]
rs1413431	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs17409213	0.81[AMR][1000 genomes]
rs17409304	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17449526	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1814203	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931360	0.81[AMR][1000 genomes]
rs272493	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs272497	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs272500	0.83[CEU][hapmap]
rs272514	0.83[CEU][hapmap]
rs35489949	0.81[AMR][1000 genomes]
rs3737673	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs3765983	0.95[CEU][hapmap];0.81[AMR][1000 genomes]
rs3820039	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs421105	0.83[CEU][hapmap]
rs5026277	0.88[CEU][hapmap]
rs56104000	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs56408800	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57160573	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57210989	0.81[AMR][1000 genomes]
rs61124915	0.81[AMR][1000 genomes]
rs72720116	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72720130	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7518184	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11161831	CLCA2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:86897200-86922800	Strong transcription	HMEC	breast
4	chr1:86897400-86906200	Strong transcription	NHEK	skin
5	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:86902000-86913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:86902200-86905800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:86902200-86906800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:86902200-86907200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:86902400-86907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:86902400-86907400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus

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