Variant report

Variant	rs7616077
Chromosome Location	chr3:53183385-53183386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53173740..53175835-chr3:53182321..53184485,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11130344	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130345	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130350	0.84[CHD][hapmap]
rs13085294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2358617	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773729	0.84[CHD][hapmap]
rs4687706	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6778939	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6778964	0.87[CHD][hapmap]
rs6807359	0.87[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7616077	PBRM1	cis	cerebellum	SCAN
rs7616077	GLT8D1	cis	cerebellum	SCAN
rs7616077	SLC38A3	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53169200-53183800	Weak transcription	Right Ventricle	heart
2	chr3:53174800-53189600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:53175000-53183800	Weak transcription	Esophagus	oesophagus
4	chr3:53175200-53183800	Weak transcription	Right Atrium	heart
5	chr3:53175400-53183600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:53175600-53184000	Weak transcription	NHDF-Ad	bronchial
7	chr3:53175800-53183800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:53176400-53188000	Enhancers	Stomach Mucosa	stomach
9	chr3:53177800-53190200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:53178000-53189600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr3:53178200-53184400	Weak transcription	Placenta	Placenta
12	chr3:53178600-53190200	Enhancers	Colonic Mucosa	Colon
13	chr3:53179000-53190000	Enhancers	Duodenum Mucosa	Duodenum
14	chr3:53179200-53186400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr3:53180000-53183800	Weak transcription	Hela-S3	cervix
16	chr3:53180600-53183800	Weak transcription	Fetal Intestine Large	intestine
17	chr3:53180600-53185400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr3:53180800-53184000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:53181200-53183600	Weak transcription	A549	lung
20	chr3:53181600-53183400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:53181600-53184000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:53181600-53184200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:53181600-53188000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:53181800-53183600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:53181800-53183600	Weak transcription	Spleen	Spleen
26	chr3:53181800-53183800	Weak transcription	Lung	lung
27	chr3:53181800-53187600	Weak transcription	Brain Anterior Caudate	brain
28	chr3:53182000-53183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:53182000-53184000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:53182200-53186600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:53182400-53183400	Weak transcription	Pancreas	Pancrea
32	chr3:53182400-53185800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:53182400-53185800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:53182400-53187800	Weak transcription	Small Intestine	intestine
35	chr3:53182400-53193400	Weak transcription	Psoas Muscle	Psoas
36	chr3:53182400-53193800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:53182600-53183600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:53182600-53183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:53182600-53184200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:53183200-53194600	Enhancers	Gastric	stomach

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