Variant report

Variant	rs10518812
Chromosome Location	chr15:43652937-43652938
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43645456..43647561-chr15:43650775..43652983,2	K562	blood:
2	chr15:43621538..43624484-chr15:43650651..43653663,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168806	Chromatin interaction
ENSG00000168803	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1095386	1.00[YRI][hapmap]
rs12899865	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12900259	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12905220	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12906017	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12906481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907870	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908460	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12911569	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12911740	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12912744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12913977	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12914122	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16957680	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16957715	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957730	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17723479	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17780417	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17780920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1814324	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1814538	0.94[YRI][hapmap]
rs2230451	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2242069	0.94[YRI][hapmap]
rs2264876	0.94[YRI][hapmap]
rs2439832	0.94[YRI][hapmap]
rs2439850	0.94[YRI][hapmap]
rs2444032	0.94[YRI][hapmap]
rs2444250	0.94[YRI][hapmap]
rs2467736	0.94[YRI][hapmap]
rs2467739	0.94[YRI][hapmap]
rs34002293	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34178146	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34181131	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34212866	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34515241	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591748	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34633582	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34657657	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34661349	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34697113	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34715468	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34767197	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860428	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34921640	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35158584	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35160541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35278805	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35311230	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35326382	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35681736	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35903301	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35958032	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35975365	0.93[EUR][1000 genomes]
rs35992154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36078097	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3862138	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.81[MEX][hapmap]
rs495175	0.94[YRI][hapmap]
rs514438	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs537115	0.94[YRI][hapmap]
rs55748552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55801120	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57728767	0.83[AFR][1000 genomes]
rs60018990	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62019432	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62019442	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62020574	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62020575	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62021176	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62021180	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66629206	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689647	0.94[YRI][hapmap]
rs689781	0.94[YRI][hapmap]
rs689826	0.94[YRI][hapmap]
rs689835	0.94[YRI][hapmap]
rs690316	0.94[YRI][hapmap]
rs690466	0.94[YRI][hapmap]
rs7048	0.82[ASW][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap]
rs71476435	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7168220	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173383	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176923	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177146	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7177892	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7180812	0.82[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181545	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7181634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181783	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7182292	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7183708	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72707530	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72709850	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72709879	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8027748	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs10518812	DUOXA1	cis	parietal	SCAN
rs10518812	ZSCAN29	cis	lymphoblastoid	seeQTL
rs10518812	ZSCAN29	cis	Esophagus Muscularis	GTEx
rs10518812	ZNF690	cis	multi-tissue	Pritchard
rs10518812	TUBGCP4	cis	Artery Tibial	GTEx
rs10518812	WDR76	cis	parietal	SCAN
rs10518812	LCMT2	cis	Esophagus Mucosa	GTEx
rs10518812	ZFP106	cis	cerebellum	SCAN
rs10518812	TGM7	cis	Esophagus Mucosa	GTEx
rs10518812	TUBGCP4	cis	cerebellum	SCAN
rs10518812	ADAL	cis	cerebellum	SCAN
rs10518812	ZSCAN29	cis	multi-tissue	Pritchard
rs10518812	FLJ35867	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43623400-43653200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:43623600-43653000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43646800-43656200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:43648800-43653000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:43649200-43655400	ZNF genes & repeats	Fetal Intestine Large	intestine
6	chr15:43649200-43658600	ZNF genes & repeats	Liver	Liver
7	chr15:43649800-43653200	Strong transcription	Placenta	Placenta
8	chr15:43649800-43654000	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr15:43649800-43660000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr15:43649800-43660200	ZNF genes & repeats	Fetal Muscle Leg	muscle
11	chr15:43650200-43653000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:43650200-43655000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:43650200-43656800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
14	chr15:43650200-43657000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr15:43650200-43657400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:43650200-43657600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
17	chr15:43650200-43657800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:43650200-43657800	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr15:43650200-43658600	ZNF genes & repeats	GM12878-XiMat	blood
20	chr15:43650200-43659800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:43650200-43660400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
22	chr15:43650200-43661600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:43650400-43653200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:43650400-43653600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:43650400-43654800	ZNF genes & repeats	HSMM	muscle
26	chr15:43650400-43655200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
27	chr15:43650400-43656200	ZNF genes & repeats	NH-A	brain
28	chr15:43650400-43656600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
29	chr15:43650400-43657000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:43650400-43657600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:43650400-43658800	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr15:43650600-43654600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
33	chr15:43650600-43655000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr15:43650600-43656600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
35	chr15:43650600-43661400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:43650800-43653000	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:43650800-43653000	Strong transcription	Brain Hippocampus Middle	brain
38	chr15:43650800-43653200	Strong transcription	Rectal Smooth Muscle	rectum
39	chr15:43650800-43654000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:43650800-43654000	Strong transcription	HepG2	liver
41	chr15:43650800-43654200	ZNF genes & repeats	NHEK	skin
42	chr15:43650800-43656400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:43650800-43656400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
44	chr15:43650800-43656400	ZNF genes & repeats	HMEC	breast
45	chr15:43650800-43656400	ZNF genes & repeats	Osteobl	bone
46	chr15:43650800-43656600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:43650800-43656800	ZNF genes & repeats	NHLF	lung
48	chr15:43650800-43657600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr15:43650800-43659800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:43650800-43660200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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