Variant report

Variant	rs12540972
Chromosome Location	chr8:90719109-90719110
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	chr8:90718183..90720246-chr8:90997582..90999794,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10956227	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956271	0.85[EUR][1000 genomes]
rs11988253	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11988552	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11995005	0.85[EUR][1000 genomes]
rs12542577	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546631	1.00[AMR][1000 genomes]
rs12681146	1.00[AFR][1000 genomes]
rs1397305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293808	0.85[EUR][1000 genomes]
rs2293809	0.85[EUR][1000 genomes]
rs719324	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7834416	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465735	chr8:89760311-90729507	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv611714	chr8:89760311-90729507	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv870380	chr8:90546585-90720182	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1026523	chr8:90558935-90722580	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv831389	chr8:90575517-90753120	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1017263	chr8:90605445-90722580	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1031578	chr8:90670102-90757821	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3340425	chr8:90686312-90722629	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
11	nsv6294	chr8:90705780-90750101	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90709000-90720200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:90710000-90730000	Weak transcription	HSMMtube	muscle
3	chr8:90710200-90729600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:90710200-90730400	Weak transcription	A549	lung
5	chr8:90710200-90731200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr8:90710200-90736200	Weak transcription	Adipose Nuclei	Adipose
7	chr8:90711200-90733800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:90711400-90720200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr8:90713200-90741200	Weak transcription	Left Ventricle	heart
10	chr8:90713400-90720400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:90713400-90738000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr8:90713600-90756200	Weak transcription	Pancreas	Pancrea
13	chr8:90713800-90720400	Weak transcription	Fetal Intestine Small	intestine
14	chr8:90713800-90721000	Weak transcription	Lung	lung
15	chr8:90714000-90719600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:90714200-90720400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr8:90714200-90728000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:90714200-90741400	Weak transcription	Right Ventricle	heart
19	chr8:90714400-90721800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr8:90714400-90741000	Weak transcription	Gastric	stomach
21	chr8:90714600-90720000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr8:90714600-90726600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr8:90714800-90733000	Weak transcription	Placenta	Placenta
24	chr8:90715000-90720200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr8:90715200-90720000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr8:90715400-90720200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:90715400-90741200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr8:90715600-90720000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr8:90715800-90720600	Weak transcription	Fetal Intestine Large	intestine
30	chr8:90716000-90720000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr8:90716000-90720400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr8:90716800-90738000	Weak transcription	Brain Hippocampus Middle	brain
33	chr8:90717200-90729600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:90717200-90733400	Weak transcription	Fetal Muscle Leg	muscle
35	chr8:90717200-90741000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr8:90717400-90720400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr8:90717400-90738000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr8:90717600-90720400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr8:90717600-90733400	Weak transcription	Aorta	Aorta
40	chr8:90717600-90733800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr8:90717800-90720400	Weak transcription	Fetal Stomach	stomach
42	chr8:90717800-90731200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:90717800-90736200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr8:90717800-90737800	Weak transcription	NHEK	skin
45	chr8:90717800-90738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr8:90717800-90738000	Weak transcription	NH-A	brain
47	chr8:90717800-90747800	Weak transcription	Ovary	ovary
48	chr8:90718200-90731000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr8:90718600-90719600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:90718600-90720200	Weak transcription	Fetal Lung	lung

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