Variant report

Variant	rs1398754
Chromosome Location	chr3:111444886-111444887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1105448	0.83[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494734	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12632310	0.81[GIH][hapmap]
rs13061461	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083322	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs13086018	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1398751	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]
rs1398753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16858448	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs17423838	0.90[LWK][hapmap];0.85[YRI][hapmap]
rs17489748	0.85[YRI][hapmap]
rs1877575	0.83[CHD][hapmap]
rs2292518	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2399394	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3922706	0.86[CEU][hapmap]
rs3922707	0.86[CEU][hapmap]
rs3922780	0.85[CEU][hapmap]
rs4075549	0.85[CEU][hapmap]
rs4401340	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4414820	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4542994	0.86[CEU][hapmap]
rs4682298	0.86[JPT][hapmap]
rs4682313	0.83[CEU][hapmap]
rs6438012	0.86[CEU][hapmap]
rs66539950	0.82[AFR][1000 genomes]
rs7624162	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627909	0.85[CEU][hapmap]
rs7646161	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7646453	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs882591	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs938219	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854875	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]
rs9871034	0.85[CEU][hapmap]

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
rs1398754	ZBED2	cis	parietal	SCAN
rs1398754	TMPRSS7	cis	parietal	SCAN

Chromatin state (count:62 , 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	chr3:111420600-111445600	Weak transcription	HepG2	liver
4	chr3:111427200-111448400	Weak transcription	Right Ventricle	heart
5	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:111428800-111445200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:111429400-111446800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:111431600-111451400	Weak transcription	Gastric	stomach
10	chr3:111432000-111448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:111432000-111448600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:111432400-111445000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:111433800-111447000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:111435200-111447800	Weak transcription	HUVEC	blood vessel
16	chr3:111436800-111448400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:111440400-111448400	Weak transcription	Right Atrium	heart
18	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
19	chr3:111441400-111448400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
21	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
23	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
24	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:111442200-111445200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:111442200-111445600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:111442400-111456000	Weak transcription	Lung	lung
29	chr3:111442600-111445000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:111442600-111446600	Weak transcription	Fetal Heart	heart
31	chr3:111442600-111448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:111442800-111446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:111442800-111447200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:111442800-111447200	Weak transcription	NHEK	skin
36	chr3:111442800-111448000	Weak transcription	Hela-S3	cervix
37	chr3:111442800-111448200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:111442800-111448400	Weak transcription	Fetal Stomach	stomach
39	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:111443000-111447000	Weak transcription	NH-A	brain
41	chr3:111443000-111447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:111443000-111447400	Weak transcription	HMEC	breast
43	chr3:111443000-111447400	Weak transcription	HSMM	muscle
44	chr3:111443000-111448000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:111443000-111448400	Weak transcription	Left Ventricle	heart
46	chr3:111443000-111448400	Weak transcription	Ovary	ovary
47	chr3:111443000-111448400	Weak transcription	A549	lung
48	chr3:111443200-111448000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:111443200-111448000	Weak transcription	NHDF-Ad	bronchial
50	chr3:111443200-111448200	Weak transcription	NHLF	lung

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