Variant report

Variant	rs6710911
Chromosome Location	chr2:73209794-73209795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1046183	0.90[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs10496188	0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13404068	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs17008541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17008565	0.90[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17008579	0.90[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17008608	0.90[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2421099	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs3849393	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58731407	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61164794	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62147718	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62147722	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62147726	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62147727	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62147728	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62147731	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62147733	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62147735	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62148129	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62148130	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66570372	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6753054	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753133	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67673165	0.97[AFR][1000 genomes];1.00[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	nsv532723	chr2:73088191-73219259	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv874266	chr2:73137991-73220138	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6710911	CCT7	cis	cerebellum	SCAN
rs6710911	TGFA	cis	cerebellum	SCAN
rs6710911	RAB11FIP5	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73161400-73210200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:73166200-73210000	Weak transcription	Colonic Mucosa	Colon
3	chr2:73168800-73226800	Weak transcription	NHLF	lung
4	chr2:73169200-73210600	Weak transcription	Pancreas	Pancrea
5	chr2:73169800-73210000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:73176600-73227400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:73177400-73209800	Weak transcription	Esophagus	oesophagus
8	chr2:73177400-73215200	Weak transcription	Osteobl	bone
9	chr2:73178000-73214800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:73181800-73215200	Weak transcription	Thymus	Thymus
11	chr2:73182800-73213000	Weak transcription	Fetal Lung	lung
12	chr2:73183200-73228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:73185000-73214400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:73188800-73211600	Weak transcription	Primary T cells from cord blood	blood
15	chr2:73190600-73234400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:73191600-73209800	Weak transcription	Aorta	Aorta
17	chr2:73193400-73210200	Weak transcription	Adipose Nuclei	Adipose
18	chr2:73193600-73221200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:73194200-73248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:73194400-73210400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:73194400-73211400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:73194600-73209800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:73194600-73210600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:73195200-73210400	Weak transcription	Fetal Intestine Large	intestine
25	chr2:73195600-73210000	Weak transcription	Fetal Stomach	stomach
26	chr2:73197400-73210000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:73198600-73220000	Weak transcription	Small Intestine	intestine
28	chr2:73199600-73209800	Weak transcription	Gastric	stomach
29	chr2:73199600-73210000	Weak transcription	Brain Substantia Nigra	brain
30	chr2:73199600-73210000	Weak transcription	HepG2	liver
31	chr2:73200800-73210200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:73201800-73210800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:73203200-73210000	Weak transcription	Brain Anterior Caudate	brain
34	chr2:73203200-73210200	Weak transcription	Fetal Brain Female	brain
35	chr2:73203200-73218400	Weak transcription	Brain Germinal Matrix	brain
36	chr2:73203400-73211200	Weak transcription	Fetal Brain Male	brain
37	chr2:73207200-73211200	Enhancers	Fetal Heart	heart
38	chr2:73207200-73213600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:73207200-73214200	Enhancers	Left Ventricle	heart
40	chr2:73207400-73210000	Enhancers	HSMMtube	muscle
41	chr2:73207600-73209800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:73207800-73209800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:73207800-73209800	Weak transcription	Spleen	Spleen
44	chr2:73207800-73211000	Weak transcription	Brain Angular Gyrus	brain
45	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:73208000-73209800	Enhancers	Hela-S3	cervix
47	chr2:73208000-73215000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:73208000-73215200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:73208000-73247600	Weak transcription	Primary B cells from cord blood	blood
50	chr2:73208200-73210000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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