Variant report

Variant	rs1398751
Chromosome Location	chr3:111447773-111447774
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];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494734	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13061461	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083322	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs13086018	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs1398753	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1398754	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16858448	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs1877575	0.81[CHD][hapmap]
rs2292518	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2399394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821919	0.87[CEU][hapmap]
rs4401340	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4414820	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682298	0.86[JPT][hapmap]
rs7624162	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7646161	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7646453	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs882591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs938219	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854875	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]

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
rs1398751	ZBED2	cis	parietal	SCAN
rs1398751	TMPRSS7	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111420400-111450600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
4	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:111431600-111451400	Weak transcription	Gastric	stomach
7	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
9	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
11	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
13	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
18	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
19	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:111442400-111456000	Weak transcription	Lung	lung
22	chr3:111442600-111448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:111442800-111448000	Weak transcription	Hela-S3	cervix
25	chr3:111442800-111448200	Weak transcription	Adipose Nuclei	Adipose
26	chr3:111442800-111448400	Weak transcription	Fetal Stomach	stomach
27	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:111443000-111448000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:111443000-111448400	Weak transcription	Left Ventricle	heart
30	chr3:111443000-111448400	Weak transcription	Ovary	ovary
31	chr3:111443000-111448400	Weak transcription	A549	lung
32	chr3:111443200-111448000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:111443200-111448000	Weak transcription	NHDF-Ad	bronchial
34	chr3:111443200-111448200	Weak transcription	NHLF	lung
35	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
36	chr3:111443400-111448000	Weak transcription	Osteobl	bone
37	chr3:111443400-111448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:111443600-111448000	Weak transcription	HSMMtube	muscle
39	chr3:111443800-111448000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:111443800-111448200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:111443800-111448400	Weak transcription	Esophagus	oesophagus
42	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:111444000-111448400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
45	chr3:111444800-111449200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:111445200-111448000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:111445200-111448000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:111445600-111448200	Enhancers	HepG2	liver
50	chr3:111446800-111448600	Weak transcription	Colon Smooth Muscle	Colon

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