Variant report

Variant	rs8107877
Chromosome Location	chr19:39238319-39238320
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000104823	Chromatin interaction
ENSG00000205076	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1031849	0.83[YRI][hapmap];0.87[AMR][1000 genomes]
rs10421863	0.90[CHB][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10424568	1.00[JPT][hapmap]
rs1060186	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11083476	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11665964	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11672576	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12462503	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12984247	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1564203	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes]
rs2080988	0.90[AMR][1000 genomes]
rs2112649	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes]
rs3786841	0.90[AMR][1000 genomes]
rs3786843	0.88[AMR][1000 genomes]
rs4347742	0.86[AMR][1000 genomes]
rs4619518	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801861	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs4802743	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes]
rs4802797	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55923191	0.81[ASN][1000 genomes]
rs57845235	0.82[AMR][1000 genomes]
rs6508813	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6508814	0.89[AMR][1000 genomes]
rs7249585	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252630	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes]
rs749701	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs752067	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs8099948	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs888997	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9304576	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9304577	0.94[JPT][hapmap]
rs936524	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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	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	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
4	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
5	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8107877	CAPN12	cis	multi-tissue	Pritchard
rs8107877	CAPN12	cis	Adipose Subcutaneous	GTEx
rs8107877	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs8107877	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs8107877	CAPN12	cis	Heart Left Ventricle	GTEx
rs8107877	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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