Variant report

Variant	rs12520272
Chromosome Location	chr5:36977801-36977802
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	chr5:36874795..36877504-chr5:36976184..36978403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164190	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10941319	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11743833	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11744960	0.85[ASN][1000 genomes]
rs11745128	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12153359	0.89[ASN][1000 genomes]
rs12187383	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12188075	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12513653	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12516349	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12520324	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12520562	0.85[ASN][1000 genomes]
rs12521488	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16903365	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16903373	0.85[ASN][1000 genomes]
rs16903403	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903413	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903419	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16903427	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16903429	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16903442	0.94[ASN][1000 genomes]
rs16903456	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903466	0.87[ASN][1000 genomes]
rs16903469	0.83[EUR][1000 genomes]
rs16903477	0.85[ASN][1000 genomes]
rs2365495	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2365838	0.94[ASN][1000 genomes]
rs3776588	0.98[ASN][1000 genomes]
rs3822471	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs56680779	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56999464	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57686895	0.85[ASN][1000 genomes]
rs60633925	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60643425	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60730034	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61638663	0.92[ASN][1000 genomes]
rs62654863	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv1033562	chr5:36927652-36994811	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1023362	chr5:36927652-37010749	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
10	nsv1017947	chr5:36927652-37017180	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv1029936	chr5:36927652-37025871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
12	nsv1029319	chr5:36928654-37017180	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
13	nsv1030883	chr5:36932448-37039857	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
14	esv1803659	chr5:36935129-37039857	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
15	nsv1034694	chr5:36946454-36991605	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1015172	chr5:36946454-36993280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1033778	chr5:36946454-36994811	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1033928	chr5:36947293-37039857	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
19	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
20	nsv881592	chr5:36954812-37027258	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
21	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
22	nsv881136	chr5:36976160-37029885	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36940600-36985400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:36946400-36978000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:36948400-36985800	Weak transcription	Colonic Mucosa	Colon
4	chr5:36948600-36996600	Weak transcription	HSMMtube	muscle
5	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:36951400-37004400	Weak transcription	Right Ventricle	heart
7	chr5:36952200-36985000	Weak transcription	Small Intestine	intestine
8	chr5:36954200-36978200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:36954200-36979800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr5:36954400-36978200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:36954400-37026400	Weak transcription	Pancreas	Pancrea
12	chr5:36954600-36979000	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:36954800-37023600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:36955200-36978200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:36955200-36978200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr5:36955400-37010400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:36957600-36985400	Weak transcription	Esophagus	oesophagus
18	chr5:36959400-36988800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:36959400-36996800	Weak transcription	Gastric	stomach
20	chr5:36961600-36978000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:36961600-36978400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:36961600-36978400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr5:36961600-36979400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr5:36962400-37028400	Weak transcription	Spleen	Spleen
25	chr5:36964000-36984800	Weak transcription	Ovary	ovary
26	chr5:36965400-36981800	Weak transcription	NHEK	skin
27	chr5:36965800-37018600	Weak transcription	Psoas Muscle	Psoas
28	chr5:36966000-36998800	Weak transcription	Fetal Heart	heart
29	chr5:36967400-36978200	Strong transcription	Placenta	Placenta
30	chr5:36967800-36978200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:36968800-36984800	Weak transcription	Fetal Stomach	stomach
32	chr5:36968800-36996200	Weak transcription	Lung	lung
33	chr5:36968800-37031200	Weak transcription	Aorta	Aorta
34	chr5:36969800-36979200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:36969800-37065000	Weak transcription	Stomach Mucosa	stomach
36	chr5:36971000-36978000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:36971000-36978000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:36971000-36978200	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:36971200-36978000	Strong transcription	Hela-S3	cervix
40	chr5:36972600-37019200	Weak transcription	Brain Angular Gyrus	brain
41	chr5:36973200-36978800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:36974200-36996400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:36974400-36978000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:36975200-36978000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:36975200-36982600	Strong transcription	Primary B cells from cord blood	blood
46	chr5:36975600-36979000	Strong transcription	Fetal Thymus	thymus
47	chr5:36975800-36978000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:36975800-36978200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr5:36975800-36978400	Strong transcription	Fetal Intestine Large	intestine
50	chr5:36976000-36979000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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