Variant report

Variant	rs6130062
Chromosome Location	chr20:40789676-40789677
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	chr20:40782305..40784731-chr20:40788079..40790643,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1014757	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs11907691	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11907769	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12625238	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13040788	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16986670	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1883376	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1883377	1.00[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs1883378	0.81[CHD][hapmap]
rs2143008	0.81[CHD][hapmap]
rs2143632	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2179336	0.81[CHD][hapmap]
rs2206169	0.81[CHD][hapmap]
rs2223426	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2223718	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2867061	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2867062	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs2867063	1.00[CEU][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs2903465	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4375930	0.80[EUR][1000 genomes]
rs6016705	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs6016706	0.97[EUR][1000 genomes]
rs6016707	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6016708	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6016709	0.96[EUR][1000 genomes]
rs6016710	1.00[CEU][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs6016711	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6016712	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6016713	0.91[EUR][1000 genomes]
rs6016722	0.82[EUR][1000 genomes]
rs6030011	0.90[CHB][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs6030017	0.92[AFR][1000 genomes]
rs6030018	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6030023	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6030026	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6030027	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6030029	0.96[EUR][1000 genomes]
rs6030035	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6030036	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6030037	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6030058	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6030061	0.92[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6030072	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6030073	0.96[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6030100	0.81[CHB][hapmap]
rs6093584	1.00[CEU][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs6093588	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6093589	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6093595	0.81[EUR][1000 genomes]
rs6093598	0.96[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6102704	0.97[EUR][1000 genomes]
rs6102713	1.00[CEU][hapmap];0.85[GIH][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs6102714	0.95[EUR][1000 genomes]
rs6124427	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6124429	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6130068	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6130071	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6130073	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6130074	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6130076	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6130081	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6513772	0.82[EUR][1000 genomes]
rs7270492	0.96[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs742290	1.00[CEU][hapmap];0.81[CHD][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs742291	0.80[CHD][hapmap]
rs979634	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6130062	ADA	cis	cerebellum	SCAN
rs6130062	CTNNBL1	cis	cerebellum	SCAN
rs6130062	SPINLW1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40788200-40790000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
2	chr20:40788600-40789800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:40788600-40790200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr20:40788600-40790800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:40789400-40789800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
6	chr20:40789400-40789800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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