Variant report

Variant	rs56107912
Chromosome Location	chr3:159506873-159506874
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:159480418..159485166-chr3:159503972..159508876,8	MCF-7	breast:
2	chr3:159506660..159510516-chr3:159511737..159514255,3	MCF-7	breast:
3	chr3:159504199..159507462-chr3:159515627..159518397,3	MCF-7	breast:
4	chr3:159490266..159491970-chr3:159504872..159507711,2	MCF-7	breast:
5	chr3:159504230..159507022-chr3:159529536..159532354,2	MCF-7	breast:
6	chr3:159504063..159506884-chr3:159510912..159512830,2	K562	blood:
7	chr3:159505829..159507763-chr3:159508214..159510388,2	K562	blood:
8	chr3:159504853..159507555-chr3:159550828..159552388,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000250588	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10936179	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1107061	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11715088	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490735	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12491535	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1497762	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553081	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010748	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169305	0.90[ASN][1000 genomes]
rs3851359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889309	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3889310	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679863	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680521	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680524	0.98[ASN][1000 genomes]
rs62270387	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62270397	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6763138	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771478	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6780187	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639937	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv4084	chr3:159492488-159513251	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159493600-159509200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:159493600-159516200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:159500400-159509200	Enhancers	HepG2	liver
4	chr3:159501000-159508000	Enhancers	Colon Smooth Muscle	Colon
5	chr3:159501800-159507600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr3:159501800-159510200	Enhancers	Fetal Intestine Large	intestine
7	chr3:159502000-159522800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:159502200-159509000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:159502400-159508000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:159502400-159508600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:159502800-159508000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:159503000-159510200	Enhancers	Fetal Intestine Small	intestine
13	chr3:159503400-159508000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:159503600-159508000	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:159503800-159509600	Enhancers	Adipose Nuclei	Adipose
16	chr3:159504000-159518600	Enhancers	Brain Hippocampus Middle	brain
17	chr3:159504200-159518400	Enhancers	Brain Substantia Nigra	brain
18	chr3:159504400-159507400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:159504400-159508000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr3:159504400-159508200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:159504400-159508200	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:159504400-159509000	Enhancers	Liver	Liver
23	chr3:159504600-159509400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:159504600-159511200	Enhancers	Brain Anterior Caudate	brain
25	chr3:159504800-159508800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:159505000-159507200	Enhancers	Small Intestine	intestine
27	chr3:159505000-159515000	Enhancers	Brain Angular Gyrus	brain
28	chr3:159505200-159507400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:159505400-159507000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:159505400-159508200	Weak transcription	Colonic Mucosa	Colon
31	chr3:159505600-159507000	Enhancers	NHEK	skin
32	chr3:159505600-159512600	Enhancers	Rectal Smooth Muscle	rectum
33	chr3:159505600-159515600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:159505800-159507000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:159505800-159507000	Weak transcription	Aorta	Aorta
36	chr3:159505800-159507400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:159505800-159508600	Weak transcription	Gastric	stomach
38	chr3:159505800-159508800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:159506000-159507200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:159506000-159508800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:159506000-159508800	Weak transcription	Right Ventricle	heart
42	chr3:159506000-159509200	Weak transcription	Lung	lung
43	chr3:159506000-159518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:159506200-159507000	Enhancers	Hela-S3	cervix
45	chr3:159506200-159507000	Enhancers	NH-A	brain
46	chr3:159506200-159507600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:159506200-159509000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:159506200-159509000	Weak transcription	NHDF-Ad	bronchial
49	chr3:159506200-159510000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:159506200-159522600	Weak transcription	Fetal Kidney	kidney

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