Variant report

Variant	rs6687934
Chromosome Location	chr1:57816011-57816012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 149 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10047071	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs10047072	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10047073	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs10047177	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10047179	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10493219	0.96[CHD][hapmap]
rs10493221	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1077424	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1077425	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889035	0.85[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889036	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10889037	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889038	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap]
rs10889039	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889040	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10889041	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889042	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs11207007	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11207010	0.86[ASN][1000 genomes]
rs11207011	0.96[CHD][hapmap];0.83[ASN][1000 genomes]
rs11207012	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207013	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207014	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207015	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207016	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207018	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207026	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs11207027	0.86[JPT][hapmap]
rs1149630	0.80[EUR][1000 genomes]
rs11585751	0.92[CHD][hapmap]
rs11588755	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11589921	0.85[ASN][1000 genomes]
rs11590708	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799925	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12067263	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12085326	0.87[ASN][1000 genomes]
rs12087888	0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs12119147	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119210	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12126723	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12137169	0.96[CHD][hapmap]
rs12139429	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12240237	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1240439	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1240442	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1240443	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12405761	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12565446	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565636	0.89[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12741210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1364444	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424462	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424463	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424464	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424465	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];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424466	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1424467	0.82[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424468	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424469	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1424470	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1504594	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1557222	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs166514	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17115686	0.96[CHD][hapmap]
rs17115750	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs17423255	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17424216	0.96[CHD][hapmap]
rs17425017	0.96[CHD][hapmap]
rs17456661	0.88[CHD][hapmap]
rs17458730	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1778032	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1809976	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1834151	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1862925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113453	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113454	0.90[ASN][1000 genomes]
rs2113456	0.93[ASN][1000 genomes]
rs2161808	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2216808	0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs2405696	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2405697	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2405994	0.92[CHD][hapmap]
rs267638	0.92[CHD][hapmap]
rs267646	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs267647	0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs267650	0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs267651	0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs269038	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs269039	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs269042	0.81[GIH][hapmap]
rs269044	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs269045	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs269048	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs269049	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs269050	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs269057	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs35804651	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738553	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs374845	0.80[EUR][1000 genomes]
rs3844041	0.84[CHD][hapmap]
rs3850549	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs3850550	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs3850552	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs3850556	0.88[CHD][hapmap]
rs3861833	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3861834	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs3896279	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap]
rs3909556	0.96[CHD][hapmap]
rs3909558	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs439378	0.81[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs499339	1.00[JPT][hapmap]
rs532926	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs540431	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs563099	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs563270	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap]
rs564951	1.00[JPT][hapmap]
rs565032	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs566847	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs567773	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs574726	1.00[JPT][hapmap]
rs61769668	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61769670	0.90[ASN][1000 genomes]
rs61769725	0.81[ASN][1000 genomes]
rs6587767	0.82[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6665166	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6668257	0.83[ASN][1000 genomes]
rs6669975	0.83[ASN][1000 genomes]
rs6677561	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687842	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs736109	0.81[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs736110	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs746937	0.81[ASW][hapmap];0.85[CEU][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.84[TSI][hapmap]
rs7513076	0.82[CHB][hapmap]
rs7535763	0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs7543805	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7547412	0.88[ASN][1000 genomes]
rs7547509	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs77510	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs77511	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs882283	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs90940	0.89[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs94216	0.81[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6687934	DAB1	cis	cerebellum	SCAN
rs6687934	C1orf168	cis	cerebellum	SCAN
rs6687934	JUN	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57800000-57826600	Weak transcription	Left Ventricle	heart
2	chr1:57808200-57822400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:57808800-57816600	Weak transcription	Right Ventricle	heart
4	chr1:57811600-57819200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:57811800-57816200	Weak transcription	Fetal Brain Male	brain
6	chr1:57812800-57817600	Enhancers	Fetal Heart	heart
7	chr1:57813600-57816200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:57814600-57819400	Weak transcription	Lung	lung
9	chr1:57814800-57817600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:57815400-57816200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:57815400-57816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:57815800-57817600	Enhancers	Fetal Brain Female	brain
13	chr1:57816000-57816200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:57816000-57816400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:57816000-57816400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:57816000-57816800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:57816000-57816800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:57816000-57817000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:57816000-57817000	Enhancers	Fetal Lung	lung
20	chr1:57816000-57817600	Enhancers	Cortex derived primary cultured neurospheres	brain

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