Variant report

Variant	rs7646453
Chromosome Location	chr3:111450169-111450170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111448469..111451104-chr3:111452736..111455582,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1105448	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494734	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632310	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs13061461	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083322	0.80[CHD][hapmap]
rs13086018	0.80[CHD][hapmap]
rs1398751	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]
rs1398753	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398754	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]
rs16858448	0.82[CHD][hapmap]
rs1877575	0.80[CHD][hapmap]
rs2292518	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2399394	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821919	0.87[CEU][hapmap]
rs4401340	0.82[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4414820	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682298	0.82[JPT][hapmap]
rs7624162	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646161	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs882591	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938219	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9854875	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]

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
rs7646453	TMPRSS7	cis	parietal	SCAN
rs7646453	ZBED2	cis	parietal	SCAN

Chromatin state (count:58 , 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	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:111428800-111451200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:111431600-111451400	Weak transcription	Gastric	stomach
6	chr3:111434000-111451200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:111440800-111451200	Weak transcription	Primary B cells from cord blood	blood
8	chr3:111441400-111451000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
10	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:111442400-111456000	Weak transcription	Lung	lung
13	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
16	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
18	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:111446800-111450200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:111447200-111451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:111447400-111450200	Enhancers	HMEC	breast
23	chr3:111447400-111451000	Weak transcription	Fetal Intestine Large	intestine
24	chr3:111447600-111451000	Weak transcription	Stomach Mucosa	stomach
25	chr3:111447800-111451200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:111448600-111451200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:111448800-111453600	Weak transcription	Right Atrium	heart
28	chr3:111448800-111454200	Weak transcription	Adipose Nuclei	Adipose
29	chr3:111449000-111453400	Weak transcription	Fetal Heart	heart
30	chr3:111449000-111453600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:111449000-111453600	Weak transcription	HUVEC	blood vessel
32	chr3:111449000-111454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:111449200-111450200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:111449200-111450800	Weak transcription	A549	lung
36	chr3:111449200-111453600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:111449200-111453600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:111449400-111451000	Weak transcription	Fetal Kidney	kidney
39	chr3:111449400-111451200	Weak transcription	Fetal Stomach	stomach
40	chr3:111449400-111453400	Weak transcription	HSMMtube	muscle
41	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:111449600-111450600	Weak transcription	HepG2	liver
43	chr3:111449600-111452600	Weak transcription	HSMM	muscle
44	chr3:111449600-111452800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:111449600-111452800	Weak transcription	Hela-S3	cervix
46	chr3:111449600-111452800	Weak transcription	Osteobl	bone
47	chr3:111449600-111453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:111449600-111453400	Weak transcription	NH-A	brain
49	chr3:111449600-111453600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:111449600-111453800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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