Variant report

Variant	rs1076776
Chromosome Location	chr20:23427399-23427400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23426997..23427916-chr20:23586801..23588394,7	MCF-7	breast:
2	chr20:23426981..23427599-chr20:23487754..23488340,2	MCF-7	breast:
3	chr20:23330412..23330928-chr20:23426987..23427635,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs12625160	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12625164	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12625999	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12626013	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1419008	1.00[LWK][hapmap]
rs17757228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17757442	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17830281	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17830565	0.82[ASN][1000 genomes]
rs1936011	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1984279	0.90[LWK][hapmap]
rs2207988	0.82[ASN][1000 genomes]
rs2207989	0.82[ASN][1000 genomes]
rs2277765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281428	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2295238	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34449811	0.81[ASN][1000 genomes]
rs34648279	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736755	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3746733	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3746737	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761274	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3761275	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3827085	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3827086	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55851398	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56094936	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56334525	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6036411	0.82[ASN][1000 genomes]
rs6036423	0.84[JPT][hapmap]
rs6036424	0.84[JPT][hapmap]
rs6048803	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6048809	0.81[ASN][1000 genomes]
rs6048810	0.82[ASN][1000 genomes]
rs6048811	0.82[ASN][1000 genomes]
rs6048813	0.82[ASN][1000 genomes]
rs6048820	0.82[ASN][1000 genomes]
rs6106656	0.82[ASN][1000 genomes]
rs6106669	0.84[JPT][hapmap]
rs6114094	0.83[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6114098	0.82[ASN][1000 genomes]
rs6114100	0.82[ASN][1000 genomes]
rs6114101	0.82[ASN][1000 genomes]
rs6114142	0.84[JPT][hapmap]
rs6114144	0.84[JPT][hapmap]
rs6132599	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6132600	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6132605	1.00[CEU][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6132606	1.00[CEU][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6132609	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132610	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132620	0.81[ASN][1000 genomes]
rs6132621	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6132622	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6132623	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6132628	0.82[ASN][1000 genomes]
rs6132631	0.84[JPT][hapmap]
rs6137901	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6137907	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137910	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137913	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137914	0.88[CEU][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137915	1.00[CEU][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137917	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6137927	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137930	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137931	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137936	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137937	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6137938	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137939	1.00[CEU][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137941	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6137945	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6137948	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6137950	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6137951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137957	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6137959	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6137960	0.82[ASN][1000 genomes]
rs6137961	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs6137962	0.82[ASN][1000 genomes]
rs6137963	0.82[ASN][1000 genomes]
rs6137964	0.82[ASN][1000 genomes]
rs6137967	0.82[ASN][1000 genomes]
rs6137975	0.84[JPT][hapmap]
rs761722	0.86[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8183135	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1076776	NXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23417200-23434800	Weak transcription	Gastric	stomach
2	chr20:23417800-23441000	Weak transcription	Right Atrium	heart
3	chr20:23423000-23432200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:23423800-23432200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:23426000-23427400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr20:23426000-23427600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:23426000-23427600	Enhancers	HMEC	breast
8	chr20:23426000-23427600	Enhancers	NH-A	brain
9	chr20:23426200-23427600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:23426200-23427800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:23426400-23427400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:23426400-23427400	Enhancers	HepG2	liver
13	chr20:23426400-23427400	Enhancers	HSMM	muscle
14	chr20:23426400-23427600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr20:23426400-23427600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr20:23426400-23427600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr20:23426400-23429600	Weak transcription	Fetal Thymus	thymus
18	chr20:23427200-23427400	Enhancers	Brain Anterior Caudate	brain
19	chr20:23427200-23427400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr20:23427200-23427800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:23427200-23427800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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