Variant report

Variant	rs6110140
Chromosome Location	chr20:14010489-14010490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:13975188..13977937-chr20:14009061..14011031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172264	Chromatin interaction
ENSG00000101251	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10485770	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485771	0.85[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[YRI][hapmap]
rs11699840	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11906598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11906933	0.82[GIH][hapmap]
rs11908401	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs11908650	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12479467	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12480372	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12481175	1.00[ASW][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12481246	0.86[ASN][1000 genomes]
rs12481405	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13433198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17191368	0.82[GIH][hapmap];0.89[MEX][hapmap]
rs17263514	0.87[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs1969777	0.82[GIH][hapmap];0.94[MEX][hapmap]
rs2180404	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273401	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2295413	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2295414	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2876713	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28794917	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2990505	0.82[GIH][hapmap]
rs3848777	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3955223	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4477989	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4813148	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4813149	0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4813150	0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4814273	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4814276	0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4814277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6042511	0.82[GIH][hapmap]
rs6079241	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6105190	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6105202	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105206	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6105211	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs6110093	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6110105	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs6110126	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6110127	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6110128	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6110130	0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6110132	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110134	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6110136	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6110137	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110142	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6110149	0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6110153	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6110154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62209485	0.88[ASN][1000 genomes]
rs73900776	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73900793	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7509383	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv526954	chr20:13995214-14055947	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6110140	ISM1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14006600-14019800	Weak transcription	Esophagus	oesophagus
2	chr20:14009200-14010800	Weak transcription	Fetal Intestine Small	intestine
3	chr20:14009200-14012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr20:14010200-14011400	Weak transcription	Fetal Heart	heart

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