Variant report

Variant	rs7620955
Chromosome Location	chr3:113809350-113809351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113808957..113811894-chr3:113824166..113826467,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11926807	0.91[CEU][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs13064372	0.95[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13064466	0.96[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13069900	0.96[CEU][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13070378	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13071100	0.96[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13086657	0.96[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13087347	0.96[CEU][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13094677	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13096290	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs1386478	0.87[CEU][hapmap]
rs2242316	0.96[CEU][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2632241	0.90[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2632259	0.82[EUR][1000 genomes]
rs324553	0.91[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs324555	0.87[CEU][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs324556	0.83[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs35745351	0.83[EUR][1000 genomes]
rs4682520	0.91[MEX][hapmap]
rs7631864	0.96[CEU][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9288990	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877352	chr3:113744010-113870078	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv877353	chr3:113789029-113879562	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7620955	CD80	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113794000-113814600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:113796200-113811000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:113799600-113813600	Weak transcription	Right Atrium	heart
4	chr3:113799800-113811400	Weak transcription	NHLF	lung
5	chr3:113802600-113811600	Weak transcription	HSMMtube	muscle
6	chr3:113805400-113809800	Weak transcription	Thymus	Thymus
7	chr3:113805400-113811400	Weak transcription	Osteobl	bone
8	chr3:113805400-113812400	Weak transcription	Hela-S3	cervix
9	chr3:113805600-113810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:113805600-113810800	Weak transcription	HUVEC	blood vessel
11	chr3:113805600-113811200	Weak transcription	HMEC	breast
12	chr3:113805600-113811400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:113805600-113811400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:113805600-113811400	Weak transcription	NHEK	skin
15	chr3:113805600-113811600	Weak transcription	Brain Germinal Matrix	brain
16	chr3:113805600-113811800	Weak transcription	Aorta	Aorta
17	chr3:113805600-113812800	Weak transcription	HSMM	muscle
18	chr3:113805600-113814800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:113805600-113814800	Weak transcription	Spleen	Spleen
20	chr3:113805800-113809600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:113805800-113809800	Weak transcription	Fetal Brain Female	brain
22	chr3:113805800-113811200	Weak transcription	Fetal Kidney	kidney
23	chr3:113805800-113811400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:113805800-113811400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:113805800-113812600	Weak transcription	Lung	lung
26	chr3:113805800-113814600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:113806000-113810600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:113806000-113811800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:113806000-113812400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:113806200-113811200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:113806200-113811400	Weak transcription	NHDF-Ad	bronchial
32	chr3:113806200-113812400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:113806200-113812600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:113806200-113814400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:113806400-113811800	Weak transcription	Fetal Lung	lung
36	chr3:113806600-113811200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:113806600-113811600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:113806800-113809400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:113806800-113810600	Weak transcription	Fetal Intestine Large	intestine
40	chr3:113806800-113810800	Weak transcription	Left Ventricle	heart
41	chr3:113806800-113811000	Weak transcription	NH-A	brain
42	chr3:113806800-113811200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:113806800-113811200	Weak transcription	Adipose Nuclei	Adipose
44	chr3:113806800-113811400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:113806800-113811400	Weak transcription	Pancreas	Pancrea
46	chr3:113806800-113812400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:113806800-113814400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:113806800-113814600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:113806800-113814800	Weak transcription	Small Intestine	intestine
50	chr3:113806800-113815600	Weak transcription	Rectal Mucosa Donor 31	rectum

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