Variant report

Variant	rs12440562
Chromosome Location	chr15:83832698-83832699
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83679489..83680165-chr15:83832055..83832883,2	K562	blood:
2	chr15:83824239..83826834-chr15:83830825..83833797,3	MCF-7	breast:
3	chr15:83832074..83835254-chr15:83836409..83839436,3	K562	blood:
4	chr15:83825010..83827114-chr15:83828912..83832901,4	K562	blood:
5	chr15:83827156..83829042-chr15:83830149..83833522,4	K562	blood:

Variant related genes	Relation type
ENSG00000166503	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1045742	0.88[CEU][hapmap]
rs10520576	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1075619	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]
rs1112404	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11259905	0.88[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11259965	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11259967	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11259968	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11259969	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11259970	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11852287	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11852408	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11852446	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11852496	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11853498	1.00[CEU][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854888	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11855639	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11855722	1.00[ASN][1000 genomes]
rs11856164	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856806	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11857428	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11857641	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11858162	0.94[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858377	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11858468	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437558	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437858	0.82[EUR][1000 genomes]
rs12437901	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438398	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12438526	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438575	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438708	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439122	0.87[GIH][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439903	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12440265	0.94[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440386	0.89[CEU][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12441006	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441409	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441575	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441847	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12441907	1.00[ASN][1000 genomes]
rs12443109	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12443424	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12591855	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12593532	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12593638	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12595330	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17361375	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17507693	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17507763	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17508610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17509233	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17567151	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17567869	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17568298	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568459	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1877024	1.00[ASN][1000 genomes]
rs1880532	0.82[EUR][1000 genomes]
rs1901544	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2034618	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3915139	1.00[ASN][1000 genomes]
rs41326445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap]
rs4300612	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4408505	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423388	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480763	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547301	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4563011	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4572349	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683536	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55691648	1.00[ASN][1000 genomes]
rs55756182	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55878453	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893521	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905779	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932429	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55933526	1.00[ASN][1000 genomes]
rs56045305	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56052029	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56352317	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57219675	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57729044	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58006707	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58281154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58396076	1.00[ASN][1000 genomes]
rs58847484	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59828448	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59896565	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60344060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60819629	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61267530	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62010162	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010164	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010165	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010166	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010170	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010172	1.00[ASN][1000 genomes]
rs62010173	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010174	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010175	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010177	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010208	1.00[ASN][1000 genomes]
rs62010212	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62010214	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62010215	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62010220	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010247	1.00[ASN][1000 genomes]
rs62010248	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62010252	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010254	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62010255	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62010258	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62011869	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62025861	0.82[AMR][1000 genomes]
rs62025914	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025915	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025919	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025921	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62025923	1.00[ASN][1000 genomes]
rs6603042	1.00[ASN][1000 genomes]
rs66619192	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66757932	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67933024	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164083	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7165114	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7165978	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166078	1.00[ASN][1000 genomes]
rs7172590	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179675	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180692	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183171	1.00[ASN][1000 genomes]
rs72755992	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495630	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495911	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8027577	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8031723	0.94[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8033380	1.00[ASN][1000 genomes]
rs8038486	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8043224	1.00[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs965263	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965264	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9707895	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[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
rs12440562	C15orf40	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83777200-83834600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:83782600-83833600	Weak transcription	Right Ventricle	heart
3	chr15:83792800-83835200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:83796400-83833000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:83797800-83832800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:83808000-83835600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:83812600-83832800	Weak transcription	Small Intestine	intestine
8	chr15:83813400-83833600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:83813800-83833800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:83818600-83835200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:83818800-83835400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:83819000-83833800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:83819800-83835000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr15:83820800-83833600	Weak transcription	Osteobl	bone
15	chr15:83820800-83834800	Weak transcription	Fetal Intestine Large	intestine
16	chr15:83821000-83834600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:83823000-83833400	Weak transcription	NHLF	lung
18	chr15:83823200-83832800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:83823400-83832800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:83825200-83833800	Weak transcription	Brain Substantia Nigra	brain
21	chr15:83825600-83834800	Weak transcription	Psoas Muscle	Psoas
22	chr15:83825800-83833800	Weak transcription	Aorta	Aorta
23	chr15:83825800-83834000	Weak transcription	Fetal Stomach	stomach
24	chr15:83825800-83835400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:83825800-83847200	Weak transcription	Left Ventricle	heart
26	chr15:83826000-83833800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:83826000-83833800	Weak transcription	Brain Anterior Caudate	brain
28	chr15:83826000-83836200	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:83826200-83833600	Weak transcription	Fetal Brain Male	brain
30	chr15:83826400-83833200	Weak transcription	NHDF-Ad	bronchial
31	chr15:83826400-83833400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:83826400-83833800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:83826400-83834600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr15:83826600-83833200	Weak transcription	NHEK	skin
35	chr15:83826800-83833200	Weak transcription	Dnd41	blood
36	chr15:83826800-83833400	Weak transcription	A549	lung
37	chr15:83826800-83834600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:83826800-83835200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:83826800-83835200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:83828000-83833200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:83829000-83833000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:83829200-83833400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:83829200-83833600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:83829400-83833000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr15:83829600-83833800	Weak transcription	GM12878-XiMat	blood
46	chr15:83830000-83833000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:83830200-83833800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:83830200-83838600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr15:83830600-83832800	Strong transcription	Fetal Brain Female	brain
50	chr15:83831400-83833400	Enhancers	Primary T cells from cord blood	blood

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