Variant report

Variant	rs6036424
Chromosome Location	chr20:23459976-23459977
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23454015..23456705-chr20:23459387..23462774,3	MCF-7	breast:
2	chr20:23459835..23462068-chr20:23463876..23466517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226344	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs12625160	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12625999	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12626013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17757228	0.84[JPT][hapmap]
rs17830281	0.84[JPT][hapmap]
rs17830565	0.88[ASN][1000 genomes]
rs1936011	0.89[JPT][hapmap]
rs2073300	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap]
rs2207988	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2207989	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236021	0.86[ASN][1000 genomes]
rs2281428	0.84[JPT][hapmap]
rs2295238	0.84[JPT][hapmap]
rs28407103	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34449811	0.87[ASN][1000 genomes]
rs34740966	0.83[ASN][1000 genomes]
rs35810824	0.85[ASN][1000 genomes]
rs36165478	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736755	0.84[JPT][hapmap]
rs3746733	0.84[JPT][hapmap]
rs3746737	0.84[JPT][hapmap]
rs3761275	0.83[JPT][hapmap]
rs3827085	0.84[JPT][hapmap]
rs57021299	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59283536	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036411	0.88[ASN][1000 genomes]
rs6036422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048803	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6048809	0.87[ASN][1000 genomes]
rs6048810	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048811	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048813	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048814	0.80[EUR][1000 genomes]
rs6048820	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048822	1.00[CEU][hapmap]
rs6048824	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048826	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083135	1.00[CEU][hapmap]
rs6106656	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6106667	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6106669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61080017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114094	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6114098	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6114100	0.88[ASN][1000 genomes]
rs6114101	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6114135	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114136	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114137	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6114138	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6114139	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114141	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114142	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132620	1.00[CEU][hapmap];0.88[ASN][1000 genomes]
rs6132621	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6132622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6132623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6132628	0.88[ASN][1000 genomes]
rs6132631	1.00[CEU][hapmap];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]
rs6137907	0.84[JPT][hapmap]
rs6137910	0.84[JPT][hapmap]
rs6137913	0.84[JPT][hapmap]
rs6137915	0.84[JPT][hapmap]
rs6137919	0.82[JPT][hapmap]
rs6137920	0.90[JPT][hapmap]
rs6137927	0.84[JPT][hapmap]
rs6137929	0.84[JPT][hapmap]
rs6137930	0.84[JPT][hapmap]
rs6137931	0.84[JPT][hapmap]
rs6137936	0.84[JPT][hapmap]
rs6137938	0.84[JPT][hapmap]
rs6137939	0.84[JPT][hapmap]
rs6137945	0.84[JPT][hapmap]
rs6137947	0.84[JPT][hapmap]
rs6137957	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6137959	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6137960	0.88[ASN][1000 genomes]
rs6137961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6137962	0.88[ASN][1000 genomes]
rs6137963	0.88[ASN][1000 genomes]
rs6137964	0.88[ASN][1000 genomes]
rs6137967	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137971	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137975	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137976	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137977	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137980	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137982	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137983	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137984	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8183135	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv470544	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv585722	chr20:23424638-23569400	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv458949	chr20:23426648-23569400	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv585723	chr20:23426648-23569400	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1057992	chr20:23430887-23565333	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv544215	chr20:23430887-23565333	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6036424	NXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23446600-23465600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:23455200-23464800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr20:23459400-23460200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr20:23459400-23460200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:23459800-23461000	Weak transcription	Esophagus	oesophagus

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