Variant report

Variant	rs269038
Chromosome Location	chr1:57847976-57847977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:57847426-57848069	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000227935	TF binding region

Extended variants
information (count: 163 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10047071	0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs10047072	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10047073	0.91[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs10047177	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10047179	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493219	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs10493221	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1077424	0.82[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1077425	0.82[ASN][1000 genomes]
rs10889035	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10889036	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10889037	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10889038	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10889039	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889040	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889041	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889042	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11207007	0.89[JPT][hapmap]
rs11207011	0.96[CHD][hapmap]
rs11207012	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11207013	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207014	0.82[ASN][1000 genomes]
rs11207015	0.82[ASN][1000 genomes]
rs11207016	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11207017	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11207018	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207021	0.82[ASN][1000 genomes]
rs11207022	0.88[ASN][1000 genomes]
rs11207026	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11207027	1.00[JPT][hapmap]
rs11579258	0.82[ASN][1000 genomes]
rs11581250	0.82[ASN][1000 genomes]
rs11585284	0.82[ASN][1000 genomes]
rs11585751	0.92[CHD][hapmap]
rs11586826	0.82[ASN][1000 genomes]
rs11588755	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11590652	0.85[ASN][1000 genomes]
rs11590708	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11799925	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12067263	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087888	0.96[CHD][hapmap]
rs12119147	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12119210	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12124445	0.82[ASN][1000 genomes]
rs12125219	0.82[ASN][1000 genomes]
rs12126723	0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs12127603	0.82[ASN][1000 genomes]
rs12136107	0.82[ASN][1000 genomes]
rs12137169	0.96[CHD][hapmap]
rs12137540	0.83[ASN][1000 genomes]
rs12139429	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs12240237	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1240442	0.82[CHB][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1240443	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405761	0.90[CHB][hapmap];0.93[ASN][1000 genomes]
rs12565446	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12565636	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12741210	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1364444	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424462	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424463	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424464	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424465	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];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1424466	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs1424467	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424468	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424469	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1424470	0.87[ASN][1000 genomes]
rs1504594	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1557222	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs166514	0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs17115685	0.82[ASN][1000 genomes]
rs17115686	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs17115750	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17423255	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17424216	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs17425017	0.96[CHD][hapmap]
rs17456661	0.88[CHD][hapmap]
rs17457873	0.82[ASN][1000 genomes]
rs17458730	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17458751	0.80[ASN][1000 genomes]
rs1778032	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1778033	0.80[ASN][1000 genomes]
rs1809976	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1834151	0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1862925	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2052615	0.85[ASN][1000 genomes]
rs2052616	0.85[ASN][1000 genomes]
rs2052617	0.82[ASN][1000 genomes]
rs2113453	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113456	0.82[ASN][1000 genomes]
rs2216808	0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs2405696	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs2405697	0.96[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2405994	0.92[CHD][hapmap]
rs267638	0.92[CHD][hapmap]
rs267647	0.92[CHD][hapmap]
rs267650	0.96[CHD][hapmap]
rs267651	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs269039	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269042	0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs269044	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs269045	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs269048	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs269049	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs269050	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs269051	0.83[AMR][1000 genomes]
rs269057	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs35804651	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3738553	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3844041	0.85[CHD][hapmap]
rs3850549	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3850550	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3850552	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3850556	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs3861833	0.96[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]
rs3861834	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3896279	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3909556	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs3909557	0.88[ASN][1000 genomes]
rs3909558	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439378	0.92[CHD][hapmap];0.80[GIH][hapmap]
rs4912246	0.80[ASN][1000 genomes]
rs499339	0.89[JPT][hapmap]
rs532926	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs539310	0.80[ASN][1000 genomes]
rs540431	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs553674	0.80[ASN][1000 genomes]
rs563099	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs563270	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs564880	0.80[ASN][1000 genomes]
rs564951	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs565032	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs566847	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs567773	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs574726	0.89[JPT][hapmap]
rs61769668	0.82[ASN][1000 genomes]
rs61769725	0.90[ASN][1000 genomes]
rs6587767	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs6665166	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669975	0.92[ASN][1000 genomes]
rs6677561	0.87[ASN][1000 genomes]
rs6687842	0.82[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs6687934	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]
rs6690017	0.88[ASN][1000 genomes]
rs72674892	0.80[ASN][1000 genomes]
rs736109	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs746937	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs7513076	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs7535763	0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[ASN][1000 genomes]
rs7543805	0.82[ASN][1000 genomes]
rs7547412	0.81[ASN][1000 genomes]
rs7547509	0.86[ASN][1000 genomes]
rs77510	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs77511	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs882283	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs90940	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.86[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	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
2	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
3	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
4	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
5	nsv954	chr1:57823140-57865799	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs269038	C1orf168	cis	cerebellum	SCAN
rs269038	DAB1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57844000-57848000	Weak transcription	Fetal Heart	heart
2	chr1:57846600-57853400	Enhancers	Fetal Brain Male	brain
3	chr1:57846800-57848400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:57847000-57848000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:57847000-57850200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:57847200-57848000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:57847200-57848000	Enhancers	Fetal Brain Female	brain
8	chr1:57847400-57848000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:57847400-57848000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr1:57847400-57848200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:57847600-57848000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:57847600-57848000	Enhancers	H9 Cell Line	embryonic stem cell
13	chr1:57847600-57848000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:57847600-57848000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:57847600-57848200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:57847800-57848000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:57847800-57848600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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