Variant report

Variant	rs10501627
Chromosome Location	chr11:86351500-86351501
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10501628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898525	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11234707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11234708	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11494278	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11606017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607554	1.00[CEU][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12361283	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12362293	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12365092	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12790474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804997	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1540083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541308	0.82[ASN][1000 genomes]
rs1541309	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1541310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1938918	0.87[CHD][hapmap]
rs1938922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382935	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4944614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930619	1.00[JPT][hapmap]

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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10501627	CTSC	cis	cerebellum	SCAN
rs10501627	ME3	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86340000-86357200	Weak transcription	Fetal Brain Female	brain
2	chr11:86341000-86355400	Weak transcription	Adipose Nuclei	Adipose
3	chr11:86341600-86358800	Weak transcription	Brain Anterior Caudate	brain
4	chr11:86342200-86353200	Weak transcription	Aorta	Aorta
5	chr11:86342200-86356400	Weak transcription	Fetal Stomach	stomach
6	chr11:86344000-86373800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:86344200-86352800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:86344600-86354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:86344800-86355400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr11:86344800-86355800	Weak transcription	Pancreas	Pancrea
11	chr11:86345400-86353000	Weak transcription	HSMM	muscle
12	chr11:86346600-86351800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:86346600-86359600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:86347200-86351600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:86347200-86352600	Weak transcription	HUVEC	blood vessel
16	chr11:86348800-86351600	Enhancers	A549	lung
17	chr11:86348800-86361600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:86349400-86353600	Weak transcription	Left Ventricle	heart
19	chr11:86349400-86356000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:86349600-86353000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:86349800-86351800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:86350400-86353200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:86350400-86353200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:86350600-86352800	Weak transcription	Osteobl	bone
25	chr11:86350600-86355000	Weak transcription	HMEC	breast
26	chr11:86350600-86355000	Weak transcription	NHLF	lung
27	chr11:86350600-86355200	Weak transcription	NH-A	brain
28	chr11:86350800-86354800	Weak transcription	NHDF-Ad	bronchial
29	chr11:86350800-86355200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:86350800-86355400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:86351000-86355000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:86351200-86351800	Weak transcription	Psoas Muscle	Psoas
33	chr11:86351200-86353400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:86351400-86351800	Weak transcription	Ovary	ovary

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