Variant report

Variant	rs4802775
Chromosome Location	chr19:39234511-39234512
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39227687..39231006-chr19:39233180..39235814,6	K562	blood:
2	chr19:39227434..39229644-chr19:39233125..39236145,3	MCF-7	breast:
3	chr19:39228306..39230279-chr19:39233041..39234658,2	MCF-7	breast:
4	chr19:39233163..39234762-chr19:39351749..39353348,2	K562	blood:
5	chr19:39228662..39230704-chr19:39233193..39235780,3	K562	blood:
6	chr19:39233778..39236095-chr19:39340274..39342606,2	K562	blood:

Variant related genes	Relation type
ENSG00000267892	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000182472	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11553600	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052046	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17589415	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665451	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs41482151	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs45468197	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4802747	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67438539	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67953948	1.00[ASN][1000 genomes]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	1.00[ASN][1000 genomes]
rs73032691	1.00[ASN][1000 genomes]
rs73032697	1.00[ASN][1000 genomes]
rs73034621	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038909	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038918	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038924	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038930	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038932	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73038936	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038948	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7351086	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7507890	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs8103824	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182484	1.00[ASN][1000 genomes]
rs888995	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4802775	CAPN12	cis	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39227400-39234600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:39228400-39234600	Weak transcription	Placenta	Placenta
3	chr19:39231000-39234600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:39233000-39235200	Enhancers	HepG2	liver
5	chr19:39233200-39236000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:39234000-39235000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr19:39234200-39234600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:39234200-39234800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:39234200-39235400	Enhancers	Spleen	Spleen
10	chr19:39234400-39235000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:39234400-39235000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:39234400-39235200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:39234400-39235200	Enhancers	A549	lung
14	chr19:39234400-39236000	Enhancers	K562	blood

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