Variant report

Variant	rs2176452
Chromosome Location	chr15:92511341-92511342
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	chr15:92509487..92513090-chr15:92516971..92519490,3	MCF-7	breast:
2	chr15:92509773..92512510-chr15:92514174..92516460,3	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10454699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10852164	0.81[CEU][hapmap];0.86[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];0.90[ASN][1000 genomes]
rs12439826	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12901238	0.97[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909480	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12910715	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12910862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12916491	0.91[ASN][1000 genomes]
rs1356417	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400783	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1568210	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16946157	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16946164	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16946168	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2138849	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28470895	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35973922	0.92[ASN][1000 genomes]
rs4312282	0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4932592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4932593	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62009549	0.95[ASN][1000 genomes]
rs7165760	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171131	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7171921	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172099	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7172159	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs7178673	0.81[ASN][1000 genomes]
rs7178734	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7179815	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027160	0.86[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap]
rs8040046	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]
rs953888	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs976216	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920069	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2176452	SEMA4B	cis	parietal	SCAN
rs2176452	ZNF710	cis	parietal	SCAN
rs2176452	FANCI	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:92498200-92555000	Weak transcription	Gastric	stomach
2	chr15:92506000-92513600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr15:92506000-92517600	Weak transcription	Colonic Mucosa	Colon
4	chr15:92507600-92512200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:92507600-92514400	Enhancers	Fetal Heart	heart
6	chr15:92507600-92516400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:92507800-92513200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr15:92508000-92514000	Enhancers	Brain Angular Gyrus	brain
9	chr15:92508000-92515000	Enhancers	Brain Cingulate Gyrus	brain
10	chr15:92508600-92514200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:92508600-92517600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:92508800-92514400	Enhancers	Ovary	ovary
13	chr15:92508800-92517600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr15:92509000-92512000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr15:92509000-92518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:92509200-92513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:92509400-92511600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:92509600-92511800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:92509600-92512800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:92509600-92512800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:92509600-92512800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:92509600-92513000	Weak transcription	NHLF	lung
23	chr15:92509600-92515400	Enhancers	Brain Substantia Nigra	brain
24	chr15:92509600-92519200	Enhancers	Brain Hippocampus Middle	brain
25	chr15:92509800-92512000	Enhancers	HMEC	breast
26	chr15:92509800-92512800	Weak transcription	Adipose Nuclei	Adipose
27	chr15:92509800-92513000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:92509800-92513000	Weak transcription	HSMM	muscle
29	chr15:92509800-92515200	Enhancers	Brain Anterior Caudate	brain
30	chr15:92510000-92511600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:92510000-92513200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:92510000-92514200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:92510200-92511400	Weak transcription	Osteobl	bone
34	chr15:92510200-92511600	Weak transcription	Right Ventricle	heart
35	chr15:92510200-92511800	Weak transcription	Fetal Lung	lung
36	chr15:92510200-92511800	Weak transcription	Psoas Muscle	Psoas
37	chr15:92510200-92511800	Enhancers	Hela-S3	cervix
38	chr15:92510200-92512800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:92510200-92512800	Weak transcription	NHDF-Ad	bronchial
40	chr15:92510200-92513000	Weak transcription	HSMMtube	muscle
41	chr15:92510200-92513600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:92510800-92512000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:92510800-92512000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:92510800-92512000	Enhancers	A549	lung
45	chr15:92510800-92512000	Enhancers	NHEK	skin
46	chr15:92510800-92512200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:92510800-92512400	Enhancers	Spleen	Spleen
48	chr15:92510800-92514400	Enhancers	Left Ventricle	heart
49	chr15:92511000-92511600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr15:92511000-92514000	Enhancers	Right Atrium	heart

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