Variant report

Variant	rs12909480
Chromosome Location	chr15:92516469-92516470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:92509475..92511121-chr15:92515975..92518365,2	MCF-7	breast:
2	chr15:92515850..92520116-chr15:92521478..92524897,5	MCF-7	breast:
3	chr15:92495221..92497782-chr15:92516330..92519314,2	MCF-7	breast:
4	chr15:92397715..92399239-chr15:92515184..92517679,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10454699	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10852165	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs10852166	0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11635055	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12439826	0.96[ASN][1000 genomes]
rs12441537	1.00[YRI][hapmap]
rs12901238	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12902685	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12905744	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12910715	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12910862	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12916491	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1356417	0.96[ASN][1000 genomes]
rs1400783	0.98[ASN][1000 genomes]
rs1568210	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16946157	0.83[ASN][1000 genomes]
rs16946164	0.83[ASN][1000 genomes]
rs16946168	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs17644254	1.00[YRI][hapmap]
rs2138849	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2176452	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs28470895	0.83[ASN][1000 genomes]
rs35973922	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4312282	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4932592	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4932593	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4984325	1.00[YRI][hapmap]
rs62009549	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165760	0.91[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7171131	0.81[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7171921	0.98[ASN][1000 genomes]
rs7172099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7172159	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs7178673	0.81[ASN][1000 genomes]
rs7178734	0.96[ASN][1000 genomes]
rs7179815	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs8025658	1.00[YRI][hapmap]
rs8027160	0.85[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs8040046	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs953888	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs976216	0.96[ASN][1000 genomes]
rs9920069	0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][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	nsv1048635	chr15:92073294-92557339	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv870094	chr15:92367354-92631647	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534110	chr15:92397220-92592961	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92498200-92555000	Weak transcription	Gastric	stomach
2	chr15:92506000-92517600	Weak transcription	Colonic Mucosa	Colon
3	chr15:92508600-92517600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr15:92508800-92517600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:92509000-92518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:92509600-92519200	Enhancers	Brain Hippocampus Middle	brain
7	chr15:92512000-92516600	Weak transcription	A549	lung
8	chr15:92512200-92517600	Weak transcription	Pancreas	Pancrea
9	chr15:92512400-92517200	Weak transcription	Spleen	Spleen
10	chr15:92513400-92516600	Weak transcription	Hela-S3	cervix
11	chr15:92513800-92516600	Weak transcription	Adipose Nuclei	Adipose
12	chr15:92513800-92518400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:92513800-92518400	Weak transcription	HSMMtube	muscle
14	chr15:92514000-92516600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:92514000-92516800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:92514000-92516800	Weak transcription	Esophagus	oesophagus
17	chr15:92514000-92517600	Weak transcription	Fetal Brain Male	brain
18	chr15:92514000-92518600	Weak transcription	Psoas Muscle	Psoas
19	chr15:92514000-92523200	Weak transcription	Aorta	Aorta
20	chr15:92514200-92516800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:92514200-92518600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:92514200-92518600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:92514400-92516600	Weak transcription	Ovary	ovary
24	chr15:92515000-92516600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:92515200-92516600	Weak transcription	Brain Anterior Caudate	brain
26	chr15:92515400-92519800	Enhancers	Left Ventricle	heart
27	chr15:92515600-92519200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:92515800-92519200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr15:92515800-92519200	Enhancers	Brain Cingulate Gyrus	brain
30	chr15:92516000-92521200	Enhancers	Right Atrium	heart
31	chr15:92516200-92518200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:92516200-92519000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:92516200-92519200	Enhancers	Fetal Heart	heart
34	chr15:92516200-92519200	Enhancers	Right Ventricle	heart
35	chr15:92516400-92516600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:92516400-92516800	Flanking Active TSS	NHEK	skin
37	chr15:92516400-92518600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr15:92516400-92519200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:92516400-92519200	Enhancers	Brain Substantia Nigra	brain
40	chr15:92516400-92519200	Enhancers	Lung	lung
41	chr15:92516400-92519200	Enhancers	HMEC	breast

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