Variant report

Variant	rs10490671
Chromosome Location	chr2:36750005-36750006
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	chr2:36749468..36751853-chr2:36803823..36806536,2	K562	blood:

Variant related genes	Relation type
ENSG00000171055	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs2023408	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2888369	0.89[CHB][hapmap]
rs3770827	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770834	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3770841	0.94[CHB][hapmap]
rs3821155	0.94[ASN][1000 genomes]
rs4141686	0.89[CHB][hapmap]
rs66484476	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs711247	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs848519	1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs848520	0.93[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs848521	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs848524	1.00[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs848526	0.87[CEU][hapmap]
rs848529	0.83[CHB][hapmap]
rs848539	0.89[CHB][hapmap]
rs848543	0.89[CHB][hapmap]
rs848563	0.86[EUR][1000 genomes]
rs867701	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs884216	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs918052	0.89[CHB][hapmap]

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	nsv1010985	chr2:36707157-36942066	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv535642	chr2:36707157-36942066	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10490671	FEZ2	cis	multi-tissue	Pritchard
rs10490671	CRIM1	cis	cerebellum	SCAN
rs10490671	FEZ2	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36713800-36789600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:36720000-36760600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:36722600-36752400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:36725200-36756800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:36726800-36751800	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:36727400-36757200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:36729600-36790200	Weak transcription	Small Intestine	intestine
8	chr2:36733000-36752000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:36733200-36774200	Weak transcription	Fetal Thymus	thymus
10	chr2:36733400-36764400	Weak transcription	Pancreas	Pancrea
11	chr2:36733600-36750200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:36734600-36756800	Strong transcription	HepG2	liver
13	chr2:36735600-36754200	Strong transcription	Hela-S3	cervix
14	chr2:36735800-36751000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:36735800-36752600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:36736000-36755800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:36736400-36751400	Strong transcription	Left Ventricle	heart
18	chr2:36736800-36751400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:36737800-36750600	Strong transcription	A549	lung
20	chr2:36738200-36754000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr2:36738400-36751600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:36738400-36751600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:36738600-36754200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:36738800-36754000	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr2:36739000-36751200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:36739000-36778200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:36739200-36751200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:36739200-36751400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr2:36739200-36751600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:36739200-36751800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr2:36739400-36751000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:36739400-36757400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:36739600-36750800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:36739600-36751000	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:36739600-36751800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:36740200-36754000	Strong transcription	Adipose Nuclei	Adipose
37	chr2:36740200-36754800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:36742800-36750800	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:36743800-36751400	Strong transcription	NHEK	skin
40	chr2:36743800-36752400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:36744000-36752200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:36744000-36754200	Strong transcription	Primary hematopoietic stem cells	blood
43	chr2:36744000-36754400	Strong transcription	HMEC	breast
44	chr2:36744000-36755600	Strong transcription	NH-A	brain
45	chr2:36744000-36756600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr2:36744200-36751400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:36744200-36756600	Strong transcription	HSMM	muscle
48	chr2:36744800-36750400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:36744800-36750400	Weak transcription	Brain Anterior Caudate	brain
50	chr2:36744800-36752600	Strong transcription	NHDF-Ad	bronchial

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