Variant report

Variant	rs1981588
Chromosome Location	chr14:72039689-72039690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:72037181..72039839-chr14:72063450..72065135,2	MCF-7	breast:
2	chr14:72038823..72040937-chr14:72089563..72092048,2	MCF-7	breast:
3	chr14:72030442..72031945-chr14:72036768..72039737,2	K562	blood:
4	chr14:72036232..72038025-chr14:72039204..72041312,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction

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	0.93[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];0.93[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	0.93[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	0.93[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];1.00[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	0.93[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	0.81[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];0.93[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];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs17767680	0.93[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]
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	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214836	0.93[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	0.93[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	0.94[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	0.86[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	0.93[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	0.93[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	0.93[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	0.93[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	0.93[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	0.93[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	0.93[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];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]
rs3784066	0.93[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];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]
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];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902938	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902941	0.87[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	0.93[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	0.86[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	0.93[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];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7144299	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144829	0.94[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]
rs7152842	0.91[CEU][hapmap]
rs7154787	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154841	0.93[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	0.93[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];0.92[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8008605	0.87[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	0.94[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	0.93[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];1.00[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
rs1981588	SMOC1	cis	cerebellum	SCAN
rs1981588	PCNX	cis	cerebellum	SCAN
rs1981588	COQ6	cis	parietal	SCAN
rs1981588	PCNX	cis	parietal	SCAN
rs1981588	SIPA1L1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72022600-72040200	Weak transcription	Osteobl	bone
2	chr14:72023400-72041000	Weak transcription	HSMM	muscle
3	chr14:72024400-72052400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr14:72030400-72041000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr14:72030600-72040000	Weak transcription	Dnd41	blood
6	chr14:72030600-72048800	Weak transcription	Fetal Kidney	kidney
7	chr14:72030800-72040000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:72031000-72052600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr14:72032000-72042800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:72032200-72040000	Weak transcription	Aorta	Aorta
11	chr14:72032400-72041800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr14:72033400-72040000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr14:72033400-72040800	Weak transcription	HSMMtube	muscle
14	chr14:72033600-72041000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr14:72033800-72040000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr14:72034000-72040000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:72034000-72040200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr14:72034000-72040800	Weak transcription	Primary B cells from cord blood	blood
19	chr14:72034200-72040400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr14:72035200-72053400	Weak transcription	Spleen	Spleen
21	chr14:72035400-72041000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:72035600-72040400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:72035600-72054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr14:72036600-72040200	Weak transcription	Pancreas	Pancrea
25	chr14:72036800-72040800	Weak transcription	Primary T cells from cord blood	blood
26	chr14:72036800-72041000	Weak transcription	Brain Anterior Caudate	brain
27	chr14:72037200-72039800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr14:72037200-72051000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr14:72038000-72041800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr14:72038200-72040200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr14:72039400-72064400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr14:72039600-72042400	Enhancers	GM12878-XiMat	blood

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