Variant report

Variant	rs10409238
Chromosome Location	chr19:21888264-21888265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10415840	0.82[ASN][1000 genomes]
rs10417262	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423519	0.82[ASN][1000 genomes]
rs11671323	0.89[ASN][1000 genomes]
rs1589280	0.80[ASN][1000 genomes]
rs6511286	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248553	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3392559	chr19:21798396-21965956	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv963135	chr19:21800743-21892052	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv833783	chr19:21821406-21991838	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv1815274	chr19:21825750-21981855	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs10409238	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs10409238	ZNF100	cis	Thyroid	GTEx
rs10409238	ZNF100	cis	Artery Tibial	GTEx
rs10409238	VN1R84P	cis	Thyroid	GTEx
rs10409238	VN1R84P	cis	lung	GTEx
rs10409238	ZNF100	cis	Artery Aorta	GTEx
rs10409238	RP11-420K14.3	cis	Esophagus Muscularis	GTEx
rs10409238	VN1R84P	cis	Stomach	GTEx
rs10409238	ZNF100	cis	lung	GTEx
rs10409238	RP11-420K14.3	cis	lung	GTEx
rs10409238	ZNF100	cis	Adipose Subcutaneous	GTEx
rs10409238	ZNF100	Cis_1M	lymphoblastoid	RTeQTL
rs10409238	RP11-420K14.3	cis	Whole Blood	GTEx
rs10409238	ZNF100	cis	Nerve Tibial	GTEx
rs10409238	ZNF100	cis	Esophagus Muscularis	GTEx
rs10409238	RP11-420K14.3	cis	Adipose Subcutaneous	GTEx
rs10409238	ZNF100	cis	Skin Sun Exposed Lower leg	GTEx
rs10409238	VN1R84P	cis	Muscle Skeletal	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21880200-21888800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21887000-21888800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr19:21887000-21889200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr19:21888000-21888400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr19:21888000-21888400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:21888000-21888600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:21888000-21888800	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr19:21888200-21888600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr19:21888200-21889200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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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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