Variant report

Variant	rs1105448
Chromosome Location	chr3:111448944-111448945
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr3:111448198-111448947	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111448045..111449995-chr3:111576976..111579247,2	MCF-7	breast:
2	chr3:111448469..111451104-chr3:111452736..111455582,2	MCF-7	breast:

Variant related genes	Relation type
PLCXD2	TF binding region
PHLDB2	TF binding region
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12494734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632310	0.80[JPT][hapmap]
rs13061461	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083322	0.80[CHD][hapmap]
rs13086018	0.80[CHD][hapmap]
rs1398751	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]
rs1398753	0.83[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1398754	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]
rs16858448	0.82[CHD][hapmap]
rs1877575	0.80[CHD][hapmap]
rs2292518	0.82[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2399394	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821919	0.83[CEU][hapmap]
rs4401340	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4414820	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682298	0.82[JPT][hapmap]
rs7624162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][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]
rs7646161	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]
rs7646453	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]
rs882591	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854875	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]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1105448	TMPRSS7	cis	parietal	SCAN
rs1105448	ZBED2	cis	parietal	SCAN
rs1105448	CCDC80	cis	parietal	SCAN

Chromatin state (count:73 , 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	chr3:111441600-111449800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:111441600-111452800	Weak transcription	Placenta	Placenta
11	chr3:111442000-111450000	Weak transcription	Thymus	Thymus
12	chr3:111442000-111452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:111442400-111456000	Weak transcription	Lung	lung
15	chr3:111442600-111451200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
18	chr3:111443800-111451400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
20	chr3:111444800-111449200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:111446800-111450200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:111447000-111449600	Enhancers	NH-A	brain
24	chr3:111447200-111449400	Enhancers	NHEK	skin
25	chr3:111447200-111451200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:111447200-111451800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:111447400-111449600	Enhancers	HSMM	muscle
28	chr3:111447400-111450200	Enhancers	HMEC	breast
29	chr3:111447400-111451000	Weak transcription	Fetal Intestine Large	intestine
30	chr3:111447600-111450000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:111447600-111451000	Weak transcription	Stomach Mucosa	stomach
32	chr3:111447800-111449000	Enhancers	HUVEC	blood vessel
33	chr3:111447800-111451200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:111448000-111449000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:111448000-111449600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:111448000-111449600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:111448000-111449600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:111448000-111449600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:111448000-111449600	Enhancers	Hela-S3	cervix
40	chr3:111448000-111449600	Enhancers	Osteobl	bone
41	chr3:111448000-111449800	Enhancers	NHDF-Ad	bronchial
42	chr3:111448200-111449400	Enhancers	Brain Hippocampus Middle	brain
43	chr3:111448200-111449600	Enhancers	NHLF	lung
44	chr3:111448400-111449000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr3:111448400-111449000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:111448400-111449000	Enhancers	Brain Cingulate Gyrus	brain
47	chr3:111448400-111449000	Enhancers	Fetal Heart	heart
48	chr3:111448400-111449000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:111448400-111449200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:111448400-111449200	Enhancers	Brain Substantia Nigra	brain

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