Variant report

Variant	rs1670462
Chromosome Location	chr11:77021880-77021881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11237123	1.00[JPT][hapmap]
rs11237141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237142	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237150	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237151	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237160	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11237162	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11237164	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125619	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225478	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12361757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12363842	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363944	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap]
rs12366261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12794253	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1377472	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1597954	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1622364	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670445	0.80[EUR][1000 genomes]
rs1670446	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670450	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670455	0.82[EUR][1000 genomes]
rs1670456	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1793468	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1793471	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793472	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1793487	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1793490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602476	0.84[ASN][1000 genomes]
rs2602483	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602487	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725825	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725828	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015985	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs3015986	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3015988	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3015990	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3015992	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34880271	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4375461	0.96[ASN][1000 genomes]
rs472691	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs479104	0.84[ASN][1000 genomes]
rs493256	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs494289	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945150	1.00[JPT][hapmap]
rs4945161	0.85[CEU][hapmap]
rs508662	0.92[ASN][1000 genomes]
rs51500	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520938	0.84[AMR][1000 genomes]
rs522015	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs523481	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs535008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs552323	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557484	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs558470	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs560571	0.84[ASN][1000 genomes]
rs561386	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs562845	0.92[ASN][1000 genomes]
rs563731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs572485	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs576220	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs580624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592602	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598801	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644551	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs649040	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs653792	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66518011	0.92[ASN][1000 genomes]
rs66540426	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs66728428	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs674259	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683455	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs683762	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs684793	0.84[ASN][1000 genomes]
rs686068	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689108	0.84[ASN][1000 genomes]
rs7118943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7934230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7949721	1.00[AFR][1000 genomes]
rs883224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883680	0.96[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	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1670462	KCTD14	cis	cerebellum	SCAN
rs1670462	PAK1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77015200-77027600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr11:77020600-77024400	Weak transcription	HSMM	muscle
3	chr11:77020800-77032000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:77020800-77033200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:77021000-77022800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:77021000-77022800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr11:77021000-77024600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr11:77021000-77032600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:77021200-77022800	Weak transcription	NHDF-Ad	bronchial
10	chr11:77021600-77022400	Enhancers	Fetal Intestine Large	intestine

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