Variant report

Variant	rs12516767
Chromosome Location	chr5:179434725-179434726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179433452..179435526-chr5:179437325..179440578,3	K562	blood:
2	chr5:179427967..179430007-chr5:179432623..179435303,2	K562	blood:
3	chr5:179433452..179435407-chr5:179437744..179440525,2	K562	blood:
4	chr5:179422578..179425329-chr5:179432316..179434971,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10054689	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10067073	1.00[CEU][hapmap];0.85[YRI][hapmap]
rs10070664	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10078845	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10479556	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479558	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs10479559	1.00[CEU][hapmap]
rs10479560	1.00[CEU][hapmap]
rs10516141	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12514260	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12516233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12516364	1.00[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12516629	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13354862	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs13362131	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1345085	1.00[CEU][hapmap]
rs17079941	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1808088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4623110	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs57144908	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6881316	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6893619	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73348268	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350154	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73350172	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9654545	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179404600-179439800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:179425000-179439400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:179426200-179440000	Weak transcription	Primary T cells from cord blood	blood
7	chr5:179426400-179438400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:179426400-179447200	Weak transcription	A549	lung
9	chr5:179427000-179439600	Weak transcription	NHEK	skin
10	chr5:179427000-179447400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:179427400-179447200	Weak transcription	Hela-S3	cervix
12	chr5:179427600-179435200	Weak transcription	Small Intestine	intestine
13	chr5:179428200-179439000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:179428400-179439000	Weak transcription	HSMMtube	muscle
15	chr5:179428600-179447200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:179428800-179443400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179429000-179437800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:179429000-179447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:179429400-179447200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:179429400-179452800	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:179429600-179435000	Weak transcription	Lung	lung
23	chr5:179429600-179437400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:179429600-179438800	Weak transcription	Fetal Intestine Large	intestine
25	chr5:179429600-179439000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:179429600-179439200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:179429600-179446800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:179429600-179447000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:179429800-179434800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:179429800-179434800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr5:179429800-179434800	Weak transcription	Right Ventricle	heart
32	chr5:179429800-179437400	Weak transcription	Aorta	Aorta
33	chr5:179429800-179437400	Weak transcription	Liver	Liver
34	chr5:179429800-179437600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:179429800-179438400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr5:179429800-179439000	Weak transcription	Primary B cells from cord blood	blood
37	chr5:179429800-179445600	Weak transcription	Fetal Intestine Small	intestine
38	chr5:179429800-179446800	Weak transcription	Gastric	stomach
39	chr5:179429800-179447200	Weak transcription	Placenta	Placenta
40	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:179430000-179453000	Weak transcription	NH-A	brain
45	chr5:179430400-179435000	Weak transcription	Ovary	ovary
46	chr5:179430400-179435200	Weak transcription	Fetal Muscle Trunk	muscle
47	chr5:179430400-179437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:179430400-179437800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:179430600-179437200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:179430600-179462400	Weak transcription	HepG2	liver

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