Variant report

Variant	rs3825719
Chromosome Location	chr14:72053097-72053098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 143 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10138557	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1029570	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483836	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873246	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11848785	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1204995	0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs1204996	1.00[JPT][hapmap]
rs12127	0.82[EUR][1000 genomes]
rs12433040	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12878989	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs12879243	0.89[EUR][1000 genomes]
rs12880188	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12880291	0.82[EUR][1000 genomes]
rs12880611	0.90[EUR][1000 genomes]
rs12881643	0.87[EUR][1000 genomes]
rs12881957	0.87[EUR][1000 genomes]
rs12885344	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12887261	0.82[EUR][1000 genomes]
rs12889866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs12892512	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12894016	0.89[EUR][1000 genomes]
rs12894478	0.86[EUR][1000 genomes]
rs12896900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12896986	0.90[EUR][1000 genomes]
rs14030	0.82[EUR][1000 genomes]
rs17178206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs17178234	0.90[EUR][1000 genomes]
rs17178387	0.88[EUR][1000 genomes]
rs17767446	0.86[EUR][1000 genomes]
rs17767499	0.87[EUR][1000 genomes]
rs17767523	0.90[EUR][1000 genomes]
rs17767553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs17767680	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767686	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1859643	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108049	0.90[EUR][1000 genomes]
rs2108057	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2109276	0.90[EUR][1000 genomes]
rs2190240	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214836	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286136	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2332638	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332640	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs28859432	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33994051	0.90[EUR][1000 genomes]
rs34057981	0.82[EUR][1000 genomes]
rs34169215	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34176710	0.88[EUR][1000 genomes]
rs34281934	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34320622	0.90[EUR][1000 genomes]
rs34347034	0.89[EUR][1000 genomes]
rs34388001	0.82[EUR][1000 genomes]
rs34454371	0.89[EUR][1000 genomes]
rs34469007	0.90[EUR][1000 genomes]
rs34480562	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34524083	0.86[EUR][1000 genomes]
rs34528131	0.86[EUR][1000 genomes]
rs34748537	0.86[EUR][1000 genomes]
rs34991781	0.81[EUR][1000 genomes]
rs34993988	0.87[EUR][1000 genomes]
rs35051046	0.87[EUR][1000 genomes]
rs35231795	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35260692	0.86[EUR][1000 genomes]
rs35415083	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35468256	0.87[EUR][1000 genomes]
rs35589413	0.88[EUR][1000 genomes]
rs35609708	0.82[EUR][1000 genomes]
rs35613269	0.90[EUR][1000 genomes]
rs35620527	0.82[EUR][1000 genomes]
rs35625243	0.80[EUR][1000 genomes]
rs35680546	0.88[EUR][1000 genomes]
rs35760654	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35831373	0.81[EUR][1000 genomes]
rs35854505	0.87[EUR][1000 genomes]
rs35866366	0.81[EUR][1000 genomes]
rs35971049	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36052007	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36072220	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36093218	0.88[EUR][1000 genomes]
rs3784062	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784066	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4140797	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4319698	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4899398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902938	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902941	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902942	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55883127	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56180634	0.86[EUR][1000 genomes]
rs56407721	0.87[EUR][1000 genomes]
rs61989367	0.90[EUR][1000 genomes]
rs61989373	0.90[EUR][1000 genomes]
rs61989374	0.90[EUR][1000 genomes]
rs61989377	0.89[EUR][1000 genomes]
rs61989379	0.82[EUR][1000 genomes]
rs61989382	0.88[EUR][1000 genomes]
rs61989383	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989386	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61989417	0.81[AFR][1000 genomes]
rs61991247	0.86[EUR][1000 genomes]
rs61991248	0.86[EUR][1000 genomes]
rs61991250	0.86[EUR][1000 genomes]
rs61991254	0.86[EUR][1000 genomes]
rs61991255	0.90[EUR][1000 genomes]
rs6574015	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574016	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66645707	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67489015	0.87[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7142343	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144299	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144829	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145755	0.87[EUR][1000 genomes]
rs7147434	0.85[EUR][1000 genomes]
rs7147668	0.86[EUR][1000 genomes]
rs7148679	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7152674	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7154787	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154841	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7156313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156460	0.86[EUR][1000 genomes]
rs7157241	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs722633	0.90[EUR][1000 genomes]
rs725673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs757850	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003478	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8006300	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008605	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010616	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8013161	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8014349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017775	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323561	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9672060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498021	chr14:71874708-72128721	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3825719	COQ6	cis	parietal	SCAN
rs3825719	PCNX	cis	cerebellum	SCAN
rs3825719	PCNX	cis	parietal	SCAN
rs3825719	SIPA1L1	cis	cerebellum	SCAN
rs3825719	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72035200-72053400	Weak transcription	Spleen	Spleen
2	chr14:72035600-72054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:72039400-72064400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr14:72041400-72054200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr14:72042000-72058400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:72042000-72058600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:72042000-72058800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr14:72042000-72069400	Weak transcription	Lung	lung
9	chr14:72042200-72054400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr14:72042200-72058400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr14:72042200-72058600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr14:72042200-72058600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:72043000-72054400	Weak transcription	GM12878-XiMat	blood
14	chr14:72043400-72059200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:72049800-72063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr14:72050200-72058200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr14:72050200-72058800	Weak transcription	Small Intestine	intestine
18	chr14:72050600-72054600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr14:72051400-72054400	Weak transcription	Primary T cells from cord blood	blood
20	chr14:72051600-72061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr14:72052000-72053600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr14:72052000-72053600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr14:72052200-72053400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr14:72052400-72053200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:72052400-72053400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr14:72052400-72053800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:72052400-72053800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr14:72052400-72053800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr14:72052600-72053200	Bivalent Enhancer	Primary B cells from cord blood	blood
30	chr14:72052600-72053200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr14:72052600-72053400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr14:72052600-72053400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr14:72052600-72053400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr14:72052600-72053400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr14:72052600-72053400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:72052600-72053400	Enhancers	Fetal Intestine Small	intestine
37	chr14:72052600-72053400	Active TSS	Stomach Smooth Muscle	stomach
38	chr14:72052600-72053600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:72052600-72053600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr14:72052600-72053600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:72052600-72053600	Enhancers	Liver	Liver
42	chr14:72052600-72053600	Flanking Active TSS	Fetal Brain Female	brain
43	chr14:72052600-72053600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr14:72052600-72053600	Flanking Active TSS	HSMMtube	muscle
45	chr14:72052600-72053600	Flanking Active TSS	NH-A	brain
46	chr14:72052600-72053800	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr14:72052600-72053800	Flanking Active TSS	Osteobl	bone
48	chr14:72052600-72054400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr14:72052800-72053200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr14:72052800-72053200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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