Variant report

Variant	rs4408505
Chromosome Location	chr15:83927791-83927792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83926641..83929586-chr15:83929895..83931666,2	MCF-7	breast:
2	chr15:83925503..83927970-chr15:83932205..83935093,2	MCF-7	breast:

Extended variants
information (count: 140 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10520576	0.94[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1075619	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112404	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11259905	0.94[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11259965	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11259967	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11259968	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11259969	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11259970	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852287	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852408	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852446	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852496	0.94[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11853498	0.94[CEU][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854888	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11855639	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11855722	1.00[ASN][1000 genomes]
rs11856164	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856806	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11857428	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11857641	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11858162	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858377	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11858468	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437558	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437858	0.81[EUR][1000 genomes]
rs12437901	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438398	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12438526	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438575	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438708	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439122	0.82[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439903	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12440265	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440386	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12440562	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441006	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441409	0.94[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441575	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441847	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12441907	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12443109	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12443424	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12591855	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12593532	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12593638	0.94[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12595330	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17361375	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507693	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17507763	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17508610	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509233	0.94[CEU][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567151	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17567869	0.94[CEU][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17568298	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568459	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1877024	1.00[ASN][1000 genomes]
rs1880532	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1901544	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2034618	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3915139	1.00[ASN][1000 genomes]
rs41326445	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs4300612	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4389108	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4423388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480763	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547301	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4563011	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4572349	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683536	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55691648	1.00[ASN][1000 genomes]
rs55756182	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55878453	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893521	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905779	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932429	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933526	1.00[ASN][1000 genomes]
rs56045305	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56052029	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56352317	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57219675	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57729044	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58006707	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58281154	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58847484	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59828448	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59896565	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60344060	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819629	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267530	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62010164	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010165	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010166	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010170	1.00[ASN][1000 genomes]
rs62010172	1.00[ASN][1000 genomes]
rs62010173	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010174	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010175	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010177	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010208	1.00[ASN][1000 genomes]
rs62010212	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62010214	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62010215	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62010220	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010247	1.00[ASN][1000 genomes]
rs62010248	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62010252	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010254	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010255	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62010258	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62011869	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62025861	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62025914	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025915	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025919	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025921	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025923	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66619192	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66757932	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67933024	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164083	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7165114	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7165978	0.94[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7166078	1.00[ASN][1000 genomes]
rs7172590	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179675	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180692	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183171	1.00[ASN][1000 genomes]
rs72755992	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495630	0.94[CEU][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8027577	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8031723	0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033380	1.00[ASN][1000 genomes]
rs8038486	0.94[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8043224	0.94[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs965263	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965264	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9707895	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534418	chr15:83770116-83960718	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4408505	C15orf40	cis	parietal	SCAN
rs4408505	ANKRD34C	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83917200-83931800	Weak transcription	HSMMtube	muscle
2	chr15:83917200-83932800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:83920000-83929800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:83920000-83932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:83920800-83934400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:83923000-83929400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:83923000-83932600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:83923200-83928400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:83923200-83929200	Strong transcription	HMEC	breast
10	chr15:83923200-83931000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:83923200-83937800	Strong transcription	HSMM	muscle
12	chr15:83924000-83931600	Weak transcription	NH-A	brain
13	chr15:83924400-83930200	Strong transcription	NHEK	skin
14	chr15:83925200-83937600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:83926000-83931600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:83926800-83929400	Weak transcription	NHDF-Ad	bronchial
17	chr15:83927000-83930800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:83927000-83931600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:83927000-83931600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:83927000-83931600	Weak transcription	NHLF	lung
21	chr15:83927000-83936800	Weak transcription	Esophagus	oesophagus
22	chr15:83927200-83930000	Weak transcription	Osteobl	bone
23	chr15:83927400-83930000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:83927400-83931000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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