Variant report

Variant	rs8040046
Chromosome Location	chr15:92516612-92516613
allele	A/G
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: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10454699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10852164	0.83[CEU][hapmap];0.83[CHD][hapmap]
rs10852165	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs10852166	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11635055	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12439826	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901238	0.96[ASN][1000 genomes]
rs12902685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12903803	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12905744	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12909480	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12910715	0.95[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12910862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12916491	0.93[ASN][1000 genomes]
rs1356417	0.96[ASN][1000 genomes]
rs1400783	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1568210	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16946157	0.84[ASN][1000 genomes]
rs16946164	0.84[ASN][1000 genomes]
rs16946168	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2138849	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2176452	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28470895	0.84[ASN][1000 genomes]
rs35973922	0.93[ASN][1000 genomes]
rs4312282	0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4932592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4932593	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62009549	0.98[ASN][1000 genomes]
rs7165760	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7171131	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7171921	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172099	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7172159	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap]
rs7178673	0.81[ASN][1000 genomes]
rs7178734	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7179815	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs8027160	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs953888	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs976216	0.96[ASN][1000 genomes]
rs9920069	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8040046	SEMA4B	cis	parietal	SCAN
rs8040046	ZNF710	cis	parietal	SCAN

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	chr15:92512200-92517600	Weak transcription	Pancreas	Pancrea
8	chr15:92512400-92517200	Weak transcription	Spleen	Spleen
9	chr15:92513800-92518400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:92513800-92518400	Weak transcription	HSMMtube	muscle
11	chr15:92514000-92516800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:92514000-92516800	Weak transcription	Esophagus	oesophagus
13	chr15:92514000-92517600	Weak transcription	Fetal Brain Male	brain
14	chr15:92514000-92518600	Weak transcription	Psoas Muscle	Psoas
15	chr15:92514000-92523200	Weak transcription	Aorta	Aorta
16	chr15:92514200-92516800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:92514200-92518600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:92514200-92518600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:92515400-92519800	Enhancers	Left Ventricle	heart
20	chr15:92515600-92519200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:92515800-92519200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:92515800-92519200	Enhancers	Brain Cingulate Gyrus	brain
23	chr15:92516000-92521200	Enhancers	Right Atrium	heart
24	chr15:92516200-92518200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:92516200-92519000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:92516200-92519200	Enhancers	Fetal Heart	heart
27	chr15:92516200-92519200	Enhancers	Right Ventricle	heart
28	chr15:92516400-92516800	Flanking Active TSS	NHEK	skin
29	chr15:92516400-92518600	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr15:92516400-92519200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:92516400-92519200	Enhancers	Brain Substantia Nigra	brain
32	chr15:92516400-92519200	Enhancers	Lung	lung
33	chr15:92516400-92519200	Enhancers	HMEC	breast
34	chr15:92516600-92517000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:92516600-92517800	Enhancers	Hela-S3	cervix
36	chr15:92516600-92518000	Enhancers	Adipose Nuclei	Adipose
37	chr15:92516600-92518800	Enhancers	Ovary	ovary
38	chr15:92516600-92518800	Enhancers	A549	lung
39	chr15:92516600-92519000	Enhancers	Brain Angular Gyrus	brain
40	chr15:92516600-92519200	Enhancers	Brain Anterior Caudate	brain
41	chr15:92516600-92519200	Enhancers	Brain Inferior Temporal Lobe	brain

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