Variant report

Variant	rs10936221
Chromosome Location	chr3:100240845-100240846
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100208890..100211504-chr3:100239607..100241704,2	MCF-7	breast:
2	chr3:100240678..100242912-chr3:100244907..100246984,2	MCF-7	breast:
3	chr2:217362499..217364288-chr3:100238945..100241543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232485	Chromatin interaction
ENSG00000197756	Chromatin interaction
ENSG00000181458	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11719592	0.85[ASW][hapmap];0.94[CHB][hapmap]
rs12634317	0.94[CHB][hapmap]
rs12636452	0.94[CHB][hapmap]
rs12639465	0.89[CHB][hapmap]
rs28722928	0.83[CHB][hapmap]
rs4073343	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4075020	0.93[ASW][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs4077302	0.83[CHB][hapmap]
rs4928048	0.94[CHB][hapmap]
rs4928049	0.83[CHB][hapmap]
rs4928110	0.94[CHB][hapmap]
rs4928111	0.94[CHB][hapmap]
rs4928112	0.94[CHB][hapmap]
rs56779007	0.91[AFR][1000 genomes]
rs6441300	0.89[CHB][hapmap]
rs6441308	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs6441316	0.94[CHB][hapmap]
rs6441328	0.94[CHB][hapmap]
rs6441329	0.94[CHB][hapmap]
rs6777810	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6780654	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6792014	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6799879	0.94[CHB][hapmap]
rs6799882	0.94[CHB][hapmap]
rs6799992	0.94[CHB][hapmap]
rs6802787	0.94[CHB][hapmap]
rs6807804	0.94[CHB][hapmap]
rs6808426	0.94[CHB][hapmap]
rs7426815	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7429277	0.94[CHB][hapmap]
rs7429392	0.93[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap]
rs7431846	0.94[CHB][hapmap]
rs7433589	0.85[ASW][hapmap];0.94[CHB][hapmap]
rs7611100	0.84[CHB][hapmap]
rs7622658	0.94[CHB][hapmap]
rs7631877	0.94[CHB][hapmap]
rs7645690	0.94[CHB][hapmap]
rs7645700	0.94[CHB][hapmap]
rs7647499	1.00[CHB][hapmap]
rs7653196	0.89[CHB][hapmap]
rs9809934	0.83[CHB][hapmap]
rs9819246	0.93[CHB][hapmap]
rs9823159	0.83[CHB][hapmap]
rs9843498	0.94[CHB][hapmap]
rs9855549	0.94[CHB][hapmap]
rs9865411	0.94[CHB][hapmap]
rs9865776	0.83[CHB][hapmap]
rs9880036	0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10936221	TMEM45A	cis	lymphoblastoid	seeQTL
rs10936221	TFG	cis	multi-tissue	Pritchard
rs10936221	FAM55C	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100235200-100242000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr3:100235800-100244800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:100236400-100242600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:100237600-100241600	Weak transcription	HepG2	liver
5	chr3:100237600-100244200	Weak transcription	NH-A	brain
6	chr3:100238000-100244400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:100238000-100244400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:100238000-100252600	Weak transcription	Fetal Intestine Small	intestine
9	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
10	chr3:100238200-100244400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:100238200-100244400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:100238200-100244400	Weak transcription	HSMM	muscle
13	chr3:100238400-100244200	Weak transcription	NHDF-Ad	bronchial
14	chr3:100238800-100243800	Weak transcription	HMEC	breast
15	chr3:100239000-100241000	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:100239000-100244200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:100239000-100244600	Weak transcription	Spleen	Spleen
18	chr3:100239200-100241400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:100239200-100242200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:100239200-100243200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:100239200-100243200	Strong transcription	Fetal Lung	lung
22	chr3:100239200-100244800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:100239400-100242000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:100239400-100242200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:100239400-100242200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:100239400-100242200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr3:100239400-100242400	Strong transcription	Ovary	ovary
28	chr3:100239400-100245000	Strong transcription	Fetal Stomach	stomach
29	chr3:100239400-100245200	Strong transcription	Aorta	Aorta
30	chr3:100239600-100241200	Enhancers	Hela-S3	cervix
31	chr3:100239600-100241600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr3:100239600-100242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:100239800-100241200	Enhancers	NHEK	skin
34	chr3:100240400-100242200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:100240400-100242200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr3:100240600-100241600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:100240600-100244400	Weak transcription	Pancreas	Pancrea
38	chr3:100240800-100241000	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr3:100240800-100241200	Weak transcription	Liver	Liver
40	chr3:100240800-100241800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:100240800-100242800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:100240800-100244400	Weak transcription	Placenta	Placenta

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