Variant report

Variant	rs6130141
Chromosome Location	chr20:41093484-41093485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10451716	0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11697017	0.83[ASN][1000 genomes]
rs11700121	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12053607	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs126180	0.85[YRI][hapmap]
rs16986939	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs172981	0.85[YRI][hapmap]
rs230153	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs34142295	0.88[ASN][1000 genomes]
rs35578581	0.88[ASN][1000 genomes]
rs6016800	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6030254	0.85[EUR][1000 genomes]
rs6030257	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6030264	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6065484	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6072756	0.85[CEU][hapmap];0.94[MEX][hapmap]
rs6102839	0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs6102852	0.80[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs6124458	0.92[CHD][hapmap];0.84[JPT][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6130133	0.90[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6130134	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6130135	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6130138	0.93[CHD][hapmap];0.85[TSI][hapmap]
rs6130145	0.82[CHB][hapmap]
rs62203505	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs760704	0.85[CHD][hapmap]

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	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
3	nsv833987	chr20:41007663-41184914	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv1059852	chr20:41087948-41217672	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv544276	chr20:41087948-41217672	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6130141	LOC388796	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41089200-41094600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41091800-41096800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:41092600-41096400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:41092800-41097000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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