Variant report

Variant	rs9854875
Chromosome Location	chr3:111443003-111443004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1105448	0.96[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12494734	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13061461	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083322	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs13086018	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1398751	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398753	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398754	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16858448	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1877575	0.83[CHD][hapmap]
rs2292518	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2399394	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821919	0.87[CEU][hapmap]
rs4401340	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4414820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682298	0.86[JPT][hapmap]
rs7624162	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646161	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646453	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs882591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938219	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9854875	TMPRSS7	cis	parietal	SCAN
rs9854875	ZBED2	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111410600-111443400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
3	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:111420600-111445600	Weak transcription	HepG2	liver
5	chr3:111425800-111443800	Weak transcription	Dnd41	blood
6	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
7	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:111428800-111445200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:111429400-111446800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:111431600-111443800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:111431600-111443800	Weak transcription	Fetal Brain Female	brain
13	chr3:111431600-111451400	Weak transcription	Gastric	stomach
14	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
16	chr3:111432400-111445000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:111433600-111444000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:111433800-111447000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:111434000-111443400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
22	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:111438600-111444000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:111438800-111443200	Strong transcription	Primary T cells from cord blood	blood
25	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
26	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
27	chr3:111441000-111443200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:111441000-111443400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
31	chr3:111441600-111443200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
34	chr3:111441800-111443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:111442000-111443200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:111442000-111443400	Enhancers	Osteobl	bone
37	chr3:111442000-111443600	Enhancers	HSMMtube	muscle
38	chr3:111442000-111443800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:111442000-111444000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
41	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:111442200-111443200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:111442200-111443200	Enhancers	NHDF-Ad	bronchial
45	chr3:111442200-111443200	Enhancers	NHLF	lung
46	chr3:111442200-111443400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:111442200-111443600	Enhancers	GM12878-XiMat	blood
48	chr3:111442200-111443800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr3:111442200-111443800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:111442200-111445200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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