Variant report

Variant	rs3784064
Chromosome Location	chr14:72059551-72059552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72044399..72046285-chr14:72058005..72060824,2	K562	blood:
2	chr14:72051242..72053047-chr14:72057398..72060318,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10138557	0.98[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];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1029570	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483836	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873246	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11848785	0.94[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
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];0.87[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];0.90[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	0.87[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	0.81[AMR][1000 genomes];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];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767686	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1859643	0.96[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108049	0.90[EUR][1000 genomes]
rs2108057	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2109276	0.90[EUR][1000 genomes]
rs2190240	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214836	0.87[AFR][1000 genomes];0.94[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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332640	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332641	1.00[AFR][1000 genomes];0.98[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];0.88[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];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34176710	0.88[EUR][1000 genomes]
rs34281934	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];0.89[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];0.89[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];0.90[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];0.87[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	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36052007	0.88[EUR][1000 genomes]
rs36072220	0.87[AFR][1000 genomes];0.87[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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784066	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825719	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]
rs4140797	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4319698	0.85[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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902938	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902941	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902942	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55883127	0.87[AFR][1000 genomes];0.87[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	0.82[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	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574016	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66645707	0.88[EUR][1000 genomes]
rs67489015	0.87[EUR][1000 genomes]
rs7140501	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144299	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144829	1.00[AFR][1000 genomes];1.00[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	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7152674	0.89[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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7156313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156460	0.86[EUR][1000 genomes]
rs7157241	0.90[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	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003478	0.87[AFR][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];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008605	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010616	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8013161	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8014349	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017775	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323561	0.87[AFR][1000 genomes];0.98[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];0.87[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
rs3784064	PCNX	cis	cerebellum	SCAN
rs3784064	SIPA1L1	cis	cerebellum	SCAN
rs3784064	PCNX	cis	parietal	SCAN
rs3784064	COQ6	cis	parietal	SCAN
rs3784064	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72039400-72064400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr14:72042000-72069400	Weak transcription	Lung	lung
3	chr14:72049800-72063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:72051600-72061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr14:72053200-72061600	Weak transcription	Fetal Muscle Leg	muscle
6	chr14:72053400-72061600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:72053400-72061600	Weak transcription	Fetal Stomach	stomach
8	chr14:72053400-72064400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr14:72053400-72066400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr14:72053400-72066600	Weak transcription	Adipose Nuclei	Adipose
11	chr14:72053400-72070200	Weak transcription	Fetal Intestine Small	intestine
12	chr14:72053400-72098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:72053600-72059600	Active TSS	Fetal Brain Female	brain
14	chr14:72053600-72061600	Weak transcription	Colon Smooth Muscle	Colon
15	chr14:72053600-72062400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:72053600-72064600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:72053600-72066000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:72053600-72066200	Weak transcription	Liver	Liver
19	chr14:72053600-72066600	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr14:72053600-72068000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:72053800-72061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:72053800-72061800	Weak transcription	Fetal Kidney	kidney
23	chr14:72054000-72061200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr14:72054800-72060400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:72055000-72061400	Weak transcription	Brain Hippocampus Middle	brain
26	chr14:72055200-72060600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr14:72055200-72061600	Weak transcription	Brain Substantia Nigra	brain
28	chr14:72055200-72087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr14:72056200-72061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:72056400-72060600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr14:72057600-72059600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr14:72057600-72063200	Enhancers	Dnd41	blood
33	chr14:72057800-72059600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr14:72057800-72060600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr14:72057800-72062400	Weak transcription	Brain Germinal Matrix	brain
36	chr14:72058000-72059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr14:72058000-72059800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr14:72058000-72059800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr14:72058000-72059800	Enhancers	NH-A	brain
40	chr14:72058200-72059600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:72058200-72059800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr14:72058200-72062200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr14:72058400-72059600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr14:72058400-72059800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr14:72058400-72061200	Enhancers	Primary T cells from cord blood	blood
46	chr14:72058400-72062800	Enhancers	NHDF-Ad	bronchial
47	chr14:72058400-72063000	Enhancers	Fetal Heart	heart
48	chr14:72058600-72059800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr14:72058600-72059800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr14:72058600-72059800	Enhancers	HMEC	breast

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