Variant report

Variant	rs8109620
Chromosome Location	chr19:45662459-45662460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000189114	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000267545	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11672002	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs11672271	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs12975698	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12981729	0.82[ASN][1000 genomes]
rs12984180	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs35620552	0.80[ASN][1000 genomes]
rs3745157	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs62118469	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118470	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251736	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs8108762	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs968445	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv522341	chr19:45640124-45664218	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv520051	chr19:45660136-45664218	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8109620	BIRC8	cis	parietal	SCAN
rs8109620	IGLON5	cis	cerebellum	SCAN
rs8109620	LIN7B	cis	cerebellum	SCAN
rs8109620	VN1R4	cis	parietal	SCAN
rs8109620	NAPSB	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45657800-45663800	Weak transcription	Gastric	stomach
2	chr19:45657800-45663800	Weak transcription	Pancreas	Pancrea
3	chr19:45657800-45668200	Weak transcription	Right Atrium	heart
4	chr19:45659200-45663400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:45660200-45674000	Weak transcription	A549	lung
6	chr19:45660400-45663400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:45661000-45664000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:45661600-45662600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr19:45661600-45662600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:45661800-45662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:45661800-45662800	Weak transcription	Esophagus	oesophagus
12	chr19:45661800-45663000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:45662000-45667000	Weak transcription	Spleen	Spleen
14	chr19:45662200-45662600	Enhancers	HUVEC	blood vessel
15	chr19:45662400-45667200	Weak transcription	Primary hematopoietic stem cells	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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