Variant report

Variant	rs1075619
Chromosome Location	chr15:83781474-83781475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83777740..83781567-chr15:83783263..83786281,3	MCF-7	breast:
2	chr15:83775374..83777785-chr15:83779584..83782378,2	MCF-7	breast:
3	chr15:83731812..83734557-chr15:83779300..83781603,2	K562	blood:
4	chr15:83777307..83779024-chr15:83779702..83782289,2	K562	blood:
5	chr15:83731075..83738271-chr15:83771545..83781798,12	K562	blood:
6	chr15:83778623..83781494-chr15:83786049..83787627,2	K562	blood:

Variant related genes	Relation type
ENSG00000064726	Chromatin interaction
ENSG00000136404	Chromatin interaction
ENSG00000263643	Chromatin interaction
ENSG00000260579	Chromatin interaction

Extended variants
information (count: 144 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs1010820	0.82[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs1045742	0.88[CEU][hapmap]
rs10520576	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1112404	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11259905	0.88[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs11259965	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11259967	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11259968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11259969	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11259970	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852287	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11852408	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852446	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11852496	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11853498	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854888	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11855639	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11855722	1.00[ASN][1000 genomes]
rs11856164	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856806	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11857428	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11857641	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858162	0.94[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858377	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11858468	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437558	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437858	0.83[EUR][1000 genomes]
rs12437901	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438398	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12438526	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438575	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438708	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439122	0.87[GIH][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439903	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12440265	0.94[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440386	0.89[CEU][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12440562	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441006	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441409	1.00[CEU][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441575	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441847	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12441907	1.00[ASN][1000 genomes]
rs12442894	0.82[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs12443109	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12443424	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12591855	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12593532	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12593638	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12595330	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17361375	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507693	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17507763	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17508610	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509233	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567151	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17567869	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17568298	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568459	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1877024	1.00[ASN][1000 genomes]
rs1880532	0.80[EUR][1000 genomes]
rs1901544	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2034618	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41326445	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs4300612	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4408505	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423388	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480763	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547301	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4563011	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4572349	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683536	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55691648	1.00[ASN][1000 genomes]
rs55756182	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55878453	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893521	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905779	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932429	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933526	1.00[ASN][1000 genomes]
rs56045305	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56052029	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56352317	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57219675	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57729044	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58006707	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58281154	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58396076	1.00[ASN][1000 genomes]
rs58847484	1.00[ASN][1000 genomes]
rs59828448	1.00[ASN][1000 genomes]
rs59896565	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60344060	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819629	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267530	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62010162	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010164	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010165	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010166	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010170	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010172	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010173	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010174	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010175	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010177	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010208	1.00[ASN][1000 genomes]
rs62010212	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62010214	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62010215	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62010220	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010247	1.00[ASN][1000 genomes]
rs62010248	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62010252	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010254	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010255	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62010258	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62011869	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62025861	0.81[AMR][1000 genomes]
rs62025914	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025915	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025919	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025921	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025923	1.00[ASN][1000 genomes]
rs6603042	1.00[ASN][1000 genomes]
rs66619192	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66757932	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67933024	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164083	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7165114	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7165978	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7166078	1.00[ASN][1000 genomes]
rs7172590	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179675	1.00[ASN][1000 genomes]
rs7180692	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183171	1.00[ASN][1000 genomes]
rs72755992	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495630	1.00[CEU][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8027577	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8031723	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033380	1.00[ASN][1000 genomes]
rs8038486	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8043224	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs965263	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965264	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9707895	0.92[AMR][1000 genomes];0.95[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1075619	C15orf40	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83776800-83781800	Weak transcription	Gastric	stomach
2	chr15:83777000-83781800	Weak transcription	Aorta	Aorta
3	chr15:83777200-83798400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:83777200-83834600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:83777600-83786800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:83777800-83782800	Weak transcription	HSMM	muscle
7	chr15:83777800-83783600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:83777800-83798800	Weak transcription	HSMMtube	muscle
9	chr15:83778000-83782200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:83778000-83784200	Weak transcription	GM12878-XiMat	blood
11	chr15:83778200-83801600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:83778200-83806400	Weak transcription	Dnd41	blood
13	chr15:83778400-83782000	Weak transcription	Fetal Brain Female	brain
14	chr15:83778400-83782600	Weak transcription	Primary B cells from cord blood	blood
15	chr15:83778600-83782800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:83778600-83782800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:83778600-83797600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:83778800-83799000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:83779400-83781800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:83779400-83782000	Weak transcription	Esophagus	oesophagus
21	chr15:83779400-83782800	Weak transcription	Brain Germinal Matrix	brain
22	chr15:83779400-83812800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:83780000-83782200	Enhancers	Lung	lung
24	chr15:83780000-83810000	Weak transcription	Fetal Lung	lung
25	chr15:83780600-83798600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:83780800-83782200	Enhancers	NH-A	brain
27	chr15:83780800-83782600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:83780800-83782600	Enhancers	Spleen	Spleen
29	chr15:83780800-83783000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr15:83780800-83783200	Enhancers	Left Ventricle	heart
31	chr15:83780800-83783200	Enhancers	Right Atrium	heart
32	chr15:83780800-83783400	Enhancers	Adipose Nuclei	Adipose
33	chr15:83781000-83782000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:83781000-83782200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr15:83781000-83782600	Enhancers	Right Ventricle	heart
36	chr15:83781000-83783000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:83781000-83808200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:83781000-83808200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:83781200-83781600	Weak transcription	Fetal Stomach	stomach
40	chr15:83781200-83781800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:83781200-83781800	Enhancers	Fetal Muscle Trunk	muscle
42	chr15:83781200-83781800	Enhancers	Osteobl	bone
43	chr15:83781200-83782000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:83781200-83782000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:83781200-83782000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:83781200-83782000	Flanking Active TSS	Hela-S3	cervix
47	chr15:83781200-83782200	Flanking Active TSS	HUVEC	blood vessel
48	chr15:83781200-83782400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:83781200-83782400	Genic enhancers	Fetal Muscle Leg	muscle
50	chr15:83781200-83827200	Weak transcription	Rectal Mucosa Donor 31	rectum

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