Variant report

Variant	rs12139429
Chromosome Location	chr1:57812260-57812261
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 179 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs10047071	0.96[CHD][hapmap]
rs10047073	0.96[CHD][hapmap]
rs10493219	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs10493221	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1077424	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1077425	0.87[ASN][1000 genomes]
rs10889034	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs10889035	0.84[ASN][1000 genomes]
rs10889036	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10889037	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10889038	0.82[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap]
rs10889039	0.82[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.90[ASN][1000 genomes]
rs10889041	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10889042	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs10889043	0.81[ASN][1000 genomes]
rs10889044	0.89[CHB][hapmap]
rs11207007	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207011	0.92[CHD][hapmap]
rs11207012	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11207013	0.84[ASN][1000 genomes]
rs11207014	0.87[ASN][1000 genomes]
rs11207015	0.87[ASN][1000 genomes]
rs11207016	0.82[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs11207017	0.88[ASN][1000 genomes]
rs11207018	0.90[ASN][1000 genomes]
rs11207020	0.83[ASN][1000 genomes]
rs11207021	0.82[ASN][1000 genomes]
rs11207022	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207024	0.81[ASN][1000 genomes]
rs11207025	0.81[ASN][1000 genomes]
rs11207026	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs11207027	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11207028	0.81[ASN][1000 genomes]
rs11207029	0.81[ASN][1000 genomes]
rs11579258	0.82[ASN][1000 genomes]
rs11581250	0.82[ASN][1000 genomes]
rs11585284	0.82[ASN][1000 genomes]
rs11585751	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs11586826	0.82[ASN][1000 genomes]
rs11588755	0.86[ASN][1000 genomes]
rs11589921	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590708	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11799925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803514	0.81[ASN][1000 genomes]
rs12061812	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs12087888	0.92[CHD][hapmap]
rs12092706	0.81[ASN][1000 genomes]
rs12119147	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12119210	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12124445	0.82[ASN][1000 genomes]
rs12125219	0.82[ASN][1000 genomes]
rs12126723	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12127603	0.82[ASN][1000 genomes]
rs12136107	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12137169	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs12137540	0.80[ASN][1000 genomes]
rs12137583	0.87[ASN][1000 genomes]
rs12142821	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs12240237	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1240442	0.80[CHB][hapmap]
rs12565446	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12565636	0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs12566690	0.83[ASN][1000 genomes]
rs12741210	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1364444	0.91[ASN][1000 genomes]
rs1424462	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1424463	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1424464	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1424465	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1424466	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1424467	0.82[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs1424468	0.91[ASN][1000 genomes]
rs1424469	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1424470	0.91[ASN][1000 genomes]
rs1504594	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs166514	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17115685	0.82[ASN][1000 genomes]
rs17115686	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs17115750	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17423255	0.82[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[ASN][1000 genomes]
rs17424216	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs17425017	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs17456661	0.80[CHB][hapmap];0.92[CHD][hapmap];0.87[ASN][1000 genomes]
rs17457873	0.82[ASN][1000 genomes]
rs17458730	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17458751	0.81[ASN][1000 genomes]
rs17459384	0.89[CHB][hapmap]
rs1778032	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1778033	0.81[ASN][1000 genomes]
rs1809976	0.84[ASN][1000 genomes]
rs1834151	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1862925	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2052617	0.82[ASN][1000 genomes]
rs2113453	0.80[ASN][1000 genomes]
rs2113454	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113456	0.87[ASN][1000 genomes]
rs2161808	0.84[ASN][1000 genomes]
rs2216808	0.80[CHB][hapmap];0.96[CHD][hapmap]
rs2405697	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs2405994	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs267638	0.88[CHD][hapmap]
rs267647	0.88[CHD][hapmap]
rs267650	0.92[CHD][hapmap]
rs267651	0.83[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs269038	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs269044	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs269045	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs269048	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs269049	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs269050	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs269057	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs28706213	0.82[ASN][1000 genomes]
rs35804651	0.84[ASN][1000 genomes]
rs3738553	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs3844041	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs3850549	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs3850550	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3850552	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs3850556	0.92[CHD][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs3861833	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs3861834	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs3896279	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs3909556	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs3909557	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439378	0.88[CHD][hapmap]
rs4912162	0.87[ASN][1000 genomes]
rs4912163	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs4912237	0.87[ASN][1000 genomes]
rs4912244	0.88[CHB][hapmap]
rs4912246	0.81[ASN][1000 genomes]
rs4912247	0.81[ASN][1000 genomes]
rs499339	1.00[JPT][hapmap]
rs511115	0.81[ASN][1000 genomes]
rs515148	0.81[ASN][1000 genomes]
rs516918	0.81[ASN][1000 genomes]
rs517825	0.81[ASN][1000 genomes]
rs532926	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs539310	0.81[ASN][1000 genomes]
rs540431	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs553674	0.81[ASN][1000 genomes]
rs55863020	0.87[ASN][1000 genomes]
rs563099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs563270	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.81[ASN][1000 genomes]
rs564880	0.81[ASN][1000 genomes]
rs564951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs565032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs566847	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs567773	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs574726	1.00[JPT][hapmap]
rs61769668	0.87[ASN][1000 genomes]
rs61769670	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61769756	0.81[ASN][1000 genomes]
rs6587767	0.88[ASW][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6587768	0.81[ASN][1000 genomes]
rs6665166	0.87[ASN][1000 genomes]
rs6668257	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677561	0.91[ASN][1000 genomes]
rs6687842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687934	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs72674872	0.87[ASN][1000 genomes]
rs72674892	0.81[ASN][1000 genomes]
rs736109	0.88[CHD][hapmap]
rs746937	0.88[CHD][hapmap]
rs7513076	0.80[CHB][hapmap];0.80[ASN][1000 genomes]
rs7528735	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs7535763	0.96[CHD][hapmap]
rs7540817	0.83[ASN][1000 genomes]
rs7543805	0.87[ASN][1000 genomes]
rs7547509	0.84[ASN][1000 genomes]
rs77510	0.84[ASN][1000 genomes]
rs77511	0.84[ASN][1000 genomes]
rs882283	0.84[ASN][1000 genomes]
rs90940	0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv871968	chr1:57803349-57858319	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12139429	DAB1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
2	chr1:57803200-57816000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:57807200-57812400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:57807600-57814800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:57808200-57822400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:57808800-57816600	Weak transcription	Right Ventricle	heart
7	chr1:57810800-57814600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:57811000-57812800	Weak transcription	Fetal Brain Female	brain
9	chr1:57811600-57812800	Weak transcription	Fetal Heart	heart
10	chr1:57811600-57819200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:57811800-57812800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:57811800-57816200	Weak transcription	Fetal Brain Male	brain
13	chr1:57812000-57814200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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