Variant report

Variant	rs880028
Chromosome Location	chr7:50570136-50570137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50564851..50566745-chr7:50568557..50570240,2	K562	blood:
2	chr7:50570130..50572623-chr7:50573822..50576522,2	K562	blood:
3	chr7:50569843..50571376-chr7:50579895..50581810,2	K562	blood:
4	chr7:50565140..50566781-chr7:50570058..50572270,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1037351	0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1107743	0.82[CHB][hapmap]
rs11575282	0.82[CHB][hapmap]
rs11575286	0.82[CHB][hapmap]
rs11575313	0.82[CHB][hapmap]
rs11575321	0.82[CHB][hapmap]
rs11575322	0.82[CHB][hapmap]
rs11575338	0.82[CHB][hapmap]
rs11575375	0.94[ASN][1000 genomes]
rs11575383	0.89[JPT][hapmap]
rs11575387	0.90[JPT][hapmap]
rs11575388	0.90[JPT][hapmap]
rs11575450	0.90[JPT][hapmap]
rs11575548	0.82[CHB][hapmap]
rs1349491	0.82[CHB][hapmap]
rs17133842	0.90[JPT][hapmap]
rs17133853	0.81[JPT][hapmap]
rs17152014	0.90[JPT][hapmap]
rs17152020	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17634717	0.82[CHB][hapmap]
rs17634958	0.82[CHB][hapmap]
rs17635123	0.82[CHB][hapmap]
rs2122817	0.89[CHB][hapmap]
rs2167364	0.92[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2329367	0.82[CHB][hapmap]
rs3779084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807553	0.82[CHB][hapmap]
rs4490786	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6592961	0.81[CEU][hapmap];0.94[GIH][hapmap];0.82[EUR][1000 genomes]
rs6951648	1.00[JPT][hapmap]
rs7791875	0.90[JPT][hapmap];0.84[LWK][hapmap]
rs7808025	0.81[CEU][hapmap];0.80[EUR][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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs880028	C7orf72	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50543600-50595000	Weak transcription	Liver	Liver
2	chr7:50560800-50581000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:50565200-50570200	Weak transcription	Lung	lung
4	chr7:50565200-50572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:50566200-50576000	Weak transcription	Colonic Mucosa	Colon
7	chr7:50566200-50581200	Strong transcription	Fetal Intestine Small	intestine
8	chr7:50566400-50572600	Strong transcription	Fetal Intestine Large	intestine
9	chr7:50566800-50571400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr7:50568200-50574400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:50568400-50570200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr7:50568800-50571400	Enhancers	HMEC	breast
13	chr7:50569000-50570400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:50569000-50570600	Weak transcription	Psoas Muscle	Psoas
15	chr7:50569000-50592800	Weak transcription	HepG2	liver
16	chr7:50569200-50570400	Enhancers	Colon Smooth Muscle	Colon
17	chr7:50569400-50571000	Enhancers	Primary hematopoietic stem cells	blood
18	chr7:50569400-50571200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:50569400-50572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:50569600-50570200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr7:50569600-50570400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:50569600-50570600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr7:50569600-50570600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr7:50569600-50570800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:50569600-50571200	Enhancers	Fetal Stomach	stomach
26	chr7:50569600-50571200	Enhancers	Rectal Smooth Muscle	rectum
27	chr7:50569800-50570200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr7:50569800-50570200	Enhancers	NH-A	brain
29	chr7:50569800-50570400	Enhancers	HSMM	muscle
30	chr7:50569800-50570600	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr7:50569800-50570800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr7:50569800-50570800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:50569800-50570800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr7:50569800-50570800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:50569800-50570800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr7:50569800-50570800	Enhancers	HUVEC	blood vessel
37	chr7:50569800-50570800	Enhancers	NHDF-Ad	bronchial
38	chr7:50569800-50570800	Enhancers	NHEK	skin
39	chr7:50569800-50571000	Enhancers	Aorta	Aorta
40	chr7:50569800-50571000	Enhancers	Fetal Lung	lung
41	chr7:50569800-50571000	Enhancers	Right Atrium	heart
42	chr7:50569800-50571000	Enhancers	Osteobl	bone
43	chr7:50569800-50571200	Enhancers	Fetal Muscle Trunk	muscle
44	chr7:50569800-50571200	Enhancers	Ovary	ovary
45	chr7:50569800-50571200	Enhancers	HSMMtube	muscle
46	chr7:50570000-50570400	Flanking Active TSS	Hela-S3	cervix
47	chr7:50570000-50570800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:50570000-50570800	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr7:50570000-50571000	Enhancers	Left Ventricle	heart
50	chr7:50570000-50571000	Enhancers	Pancreas	Pancrea

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