Variant report

Variant	rs1859643
Chromosome Location	chr14:72055468-72055469
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10138557	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10139519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1029570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483836	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873246	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11848785	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1204995	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1204996	1.00[JPT][hapmap]
rs12127	0.82[EUR][1000 genomes]
rs12433040	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12878989	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12879243	0.86[EUR][1000 genomes]
rs12880188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12880291	0.82[EUR][1000 genomes]
rs12880611	0.87[EUR][1000 genomes]
rs12881643	0.84[EUR][1000 genomes]
rs12881957	0.87[EUR][1000 genomes]
rs12885344	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12887261	0.82[EUR][1000 genomes]
rs12889866	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12892512	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12894016	0.86[EUR][1000 genomes]
rs12894478	0.83[EUR][1000 genomes]
rs12896900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12896986	0.87[EUR][1000 genomes]
rs14030	0.82[EUR][1000 genomes]
rs17178206	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17178234	0.87[EUR][1000 genomes]
rs17178387	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17767446	0.84[EUR][1000 genomes]
rs17767499	0.84[EUR][1000 genomes]
rs17767523	0.87[EUR][1000 genomes]
rs17767553	0.96[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[EUR][1000 genomes]
rs17767680	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17767686	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1981588	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108049	0.87[EUR][1000 genomes]
rs2108057	0.96[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2109276	0.87[EUR][1000 genomes]
rs2190240	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214836	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286136	0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2332638	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2332640	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332641	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877729	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs28859432	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33994051	0.87[EUR][1000 genomes]
rs34169215	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34176710	0.86[EUR][1000 genomes]
rs34281934	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34320622	0.87[EUR][1000 genomes]
rs34347034	0.86[EUR][1000 genomes]
rs34388001	0.82[EUR][1000 genomes]
rs34454371	0.86[EUR][1000 genomes]
rs34469007	0.87[EUR][1000 genomes]
rs34480562	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34524083	0.84[EUR][1000 genomes]
rs34528131	0.84[EUR][1000 genomes]
rs34748537	0.84[EUR][1000 genomes]
rs34991781	0.81[EUR][1000 genomes]
rs34993988	0.87[EUR][1000 genomes]
rs35051046	0.84[EUR][1000 genomes]
rs35231795	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35260692	0.84[EUR][1000 genomes]
rs35415083	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35468256	0.84[EUR][1000 genomes]
rs35589413	0.90[EUR][1000 genomes]
rs35613269	0.87[EUR][1000 genomes]
rs35620527	0.82[EUR][1000 genomes]
rs35625243	0.80[EUR][1000 genomes]
rs35680546	0.86[EUR][1000 genomes]
rs35760654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35831373	0.81[EUR][1000 genomes]
rs35854505	0.84[EUR][1000 genomes]
rs35971049	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36052007	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36072220	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36093218	0.86[EUR][1000 genomes]
rs3784062	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3784064	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784066	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3825719	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140797	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4319698	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4899398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902938	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902941	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902942	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55883127	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56180634	0.88[EUR][1000 genomes]
rs56407721	0.87[EUR][1000 genomes]
rs61989367	0.87[EUR][1000 genomes]
rs61989373	0.87[EUR][1000 genomes]
rs61989374	0.87[EUR][1000 genomes]
rs61989377	0.86[EUR][1000 genomes]
rs61989379	0.82[EUR][1000 genomes]
rs61989382	0.91[EUR][1000 genomes]
rs61989383	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61989386	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61991247	0.84[EUR][1000 genomes]
rs61991248	0.84[EUR][1000 genomes]
rs61991250	0.84[EUR][1000 genomes]
rs61991254	0.83[EUR][1000 genomes]
rs61991255	0.87[EUR][1000 genomes]
rs6574015	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6574016	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66645707	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67489015	0.87[EUR][1000 genomes]
rs7140501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7142343	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144299	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144829	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145755	0.84[EUR][1000 genomes]
rs7147434	0.82[EUR][1000 genomes]
rs7147668	0.84[EUR][1000 genomes]
rs7148679	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7152674	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7154787	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154841	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7156313	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156460	0.84[EUR][1000 genomes]
rs7157241	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs722633	0.87[EUR][1000 genomes]
rs725673	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs757850	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8003478	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8006300	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8008605	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010616	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8013161	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8014349	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017775	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323561	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9672060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1859643	SMOC1	cis	cerebellum	SCAN
rs1859643	PCNX	cis	cerebellum	SCAN
rs1859643	PCNX	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72039400-72064400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr14:72042000-72058400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr14:72042000-72058600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr14:72042000-72058800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr14:72042000-72069400	Weak transcription	Lung	lung
6	chr14:72042200-72058400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:72042200-72058600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr14:72042200-72058600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr14:72043400-72059200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:72049800-72063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr14:72050200-72058200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr14:72050200-72058800	Weak transcription	Small Intestine	intestine
13	chr14:72051600-72061600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr14:72053000-72057600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:72053000-72058000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr14:72053000-72058600	Weak transcription	Thymus	Thymus
17	chr14:72053200-72058600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr14:72053200-72058600	Weak transcription	Stomach Mucosa	stomach
19	chr14:72053200-72058800	Weak transcription	Left Ventricle	heart
20	chr14:72053200-72059200	Weak transcription	Right Ventricle	heart
21	chr14:72053200-72061600	Weak transcription	Fetal Muscle Leg	muscle
22	chr14:72053400-72056000	Weak transcription	Colonic Mucosa	Colon
23	chr14:72053400-72058600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr14:72053400-72058800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:72053400-72059200	Weak transcription	Fetal Intestine Large	intestine
26	chr14:72053400-72061600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr14:72053400-72061600	Weak transcription	Fetal Stomach	stomach
28	chr14:72053400-72064400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr14:72053400-72066400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr14:72053400-72066600	Weak transcription	Adipose Nuclei	Adipose
31	chr14:72053400-72070200	Weak transcription	Fetal Intestine Small	intestine
32	chr14:72053400-72098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:72053600-72056800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr14:72053600-72058800	Weak transcription	Aorta	Aorta
35	chr14:72053600-72058800	Weak transcription	Spleen	Spleen
36	chr14:72053600-72059600	Active TSS	Fetal Brain Female	brain
37	chr14:72053600-72061600	Weak transcription	Colon Smooth Muscle	Colon
38	chr14:72053600-72062400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr14:72053600-72064600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:72053600-72066000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:72053600-72066200	Weak transcription	Liver	Liver
42	chr14:72053600-72066600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr14:72053600-72068000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr14:72053800-72056200	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr14:72053800-72058200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:72053800-72059400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr14:72053800-72061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:72053800-72061800	Weak transcription	Fetal Kidney	kidney
49	chr14:72054000-72055600	Weak transcription	Brain Anterior Caudate	brain
50	chr14:72054000-72055800	Weak transcription	Brain Germinal Matrix	brain

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