Variant report

Variant	rs8107416
Chromosome Location	chr19:39237950-39237951
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39237880-39238221	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39236154..39238526-chr19:39239272..39240879,2	K562	blood:
2	chr19:39236132..39238637-chr19:39263161..39265778,2	K562	blood:
3	chr19:39236238..39239622-chr19:39320803..39323226,4	MCF-7	breast:

Variant related genes	Relation type
CAPN12	TF binding region
ENSG00000104823	Chromatin interaction
ENSG00000205076	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10403540	0.83[EUR][1000 genomes]
rs10407371	0.87[EUR][1000 genomes]
rs10415219	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs10415646	0.80[EUR][1000 genomes]
rs10416718	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10418728	0.88[EUR][1000 genomes]
rs10421560	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11083475	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11673323	0.86[EUR][1000 genomes]
rs12460849	0.92[CEU][hapmap]
rs12462270	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs13344413	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs16972767	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs2279144	0.88[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs2303040	0.92[CEU][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs28488032	0.84[EUR][1000 genomes]
rs28624276	0.84[EUR][1000 genomes]
rs3745859	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs3786835	0.92[CEU][hapmap]
rs3786839	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs3786845	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs3786848	0.83[EUR][1000 genomes]
rs3786851	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs55873140	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55923191	0.95[EUR][1000 genomes]
rs55945853	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56172450	0.94[EUR][1000 genomes]
rs62120083	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62120087	0.91[EUR][1000 genomes]
rs7251903	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs7254100	0.91[CEU][hapmap]
rs883394	0.83[EUR][1000 genomes]
rs883433	0.92[CEU][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs9304578	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs979971	0.92[CEU][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs979972	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8107416	ERCC1	cis	cerebellum	SCAN
rs8107416	LGALS17A	cis	cerebellum	SCAN
rs8107416	ZNF526	cis	cerebellum	SCAN
rs8107416	MEGF8	cis	parietal	SCAN
rs8107416	CAPN12	cis	lung	GTEx
rs8107416	TMEM145	cis	parietal	SCAN
rs8107416	PSG3	cis	parietal	SCAN
rs8107416	CAPN12	cis	Esophagus Muscularis	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39235200-39244400	Weak transcription	HepG2	liver
2	chr19:39236000-39240800	Weak transcription	K562	blood
3	chr19:39236600-39245600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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