Variant report

Variant	rs6574016
Chromosome Location	chr14:72040525-72040526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72038823..72040937-chr14:72089563..72092048,2	MCF-7	breast:
2	chr14:72036232..72038025-chr14:72039204..72041312,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L1-2	chr14:72040206-72041803	NONHSAT037640

Extended variants
information (count: 145 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10133626	1.00[JPT][hapmap]
rs10135680	1.00[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];1.00[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	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10873246	0.86[AFR][1000 genomes];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	1.00[AFR][1000 genomes];0.98[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];0.94[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	1.00[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[AFR][1000 genomes];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];1.00[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];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];0.90[EUR][1000 genomes]
rs17767680	1.00[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];1.00[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];0.93[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]
rs2108707	0.84[EUR][1000 genomes]
rs2109276	0.90[EUR][1000 genomes]
rs2190240	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214836	1.00[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	1.00[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	0.87[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	0.93[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	1.00[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	1.00[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	1.00[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	1.00[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	1.00[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	1.00[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	1.00[AFR][1000 genomes];0.92[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];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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784066	1.00[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];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];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140797	0.86[AFR][1000 genomes];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];0.83[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];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902938	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902941	0.93[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	1.00[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	0.93[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]
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];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144299	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144829	0.87[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	0.86[AFR][1000 genomes];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]
rs7152842	0.91[CEU][hapmap]
rs7154787	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154841	1.00[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	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8006300	0.91[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008605	0.93[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	0.87[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	1.00[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];0.94[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
rs6574016	SMOC1	cis	cerebellum	SCAN
rs6574016	SIPA1L1	cis	cerebellum	SCAN
rs6574016	COQ6	cis	parietal	SCAN
rs6574016	PCNX	cis	cerebellum	SCAN
rs6574016	PCNX	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72023400-72041000	Weak transcription	HSMM	muscle
2	chr14:72024400-72052400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr14:72030400-72041000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr14:72030600-72048800	Weak transcription	Fetal Kidney	kidney
5	chr14:72031000-72052600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr14:72032000-72042800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:72032400-72041800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr14:72033400-72040800	Weak transcription	HSMMtube	muscle
9	chr14:72033600-72041000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr14:72034000-72040800	Weak transcription	Primary B cells from cord blood	blood
11	chr14:72035200-72053400	Weak transcription	Spleen	Spleen
12	chr14:72035400-72041000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:72035600-72054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr14:72036800-72040800	Weak transcription	Primary T cells from cord blood	blood
15	chr14:72036800-72041000	Weak transcription	Brain Anterior Caudate	brain
16	chr14:72037200-72051000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr14:72038000-72041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr14:72039400-72064400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr14:72039600-72042400	Enhancers	GM12878-XiMat	blood
20	chr14:72040000-72040800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr14:72040000-72041200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr14:72040000-72042000	Enhancers	Dnd41	blood
23	chr14:72040000-72042800	Enhancers	Fetal Stomach	stomach
24	chr14:72040000-72043200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr14:72040000-72043600	Enhancers	Fetal Heart	heart
26	chr14:72040000-72044200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr14:72040200-72041200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:72040200-72041400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr14:72040200-72042200	Enhancers	Primary B cells from peripheral blood	blood
30	chr14:72040200-72042200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr14:72040200-72043000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr14:72040200-72043200	Enhancers	Fetal Lung	lung
33	chr14:72040200-72043400	Enhancers	Brain Hippocampus Middle	brain
34	chr14:72040200-72043400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr14:72040200-72043400	Enhancers	Osteobl	bone
36	chr14:72040400-72041000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr14:72040400-72041000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr14:72040400-72041800	Weak transcription	Aorta	Aorta
39	chr14:72040400-72042000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr14:72040400-72042000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:72040400-72042000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr14:72040400-72042400	Enhancers	Colon Smooth Muscle	Colon
43	chr14:72040400-72043400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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