Variant report

Variant	rs17742101
Chromosome Location	chr11:36336633-36336634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1005985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10501150	1.00[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs12293053	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374377	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446670	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs1975541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs2166532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7943002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs9971501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17742101	GLDC	trans	lymphoblastoid	seeQTL
rs17742101	WT1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36332000-36338600	Weak transcription	Gastric	stomach
2	chr11:36333800-36336800	Enhancers	Fetal Intestine Small	intestine
3	chr11:36333800-36337200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:36334200-36339800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:36335000-36337200	Enhancers	Brain Substantia Nigra	brain
6	chr11:36335000-36338000	Enhancers	Adipose Nuclei	Adipose
7	chr11:36335200-36339600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr11:36335400-36340200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:36335600-36339200	Weak transcription	Colonic Mucosa	Colon
10	chr11:36335800-36337000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:36336000-36337800	Enhancers	Brain Hippocampus Middle	brain
12	chr11:36336200-36337400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr11:36336200-36340000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:36336200-36340200	Weak transcription	Brain Angular Gyrus	brain
15	chr11:36336400-36337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:36336400-36338600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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