Variant report

Variant	rs7139255
Chromosome Location	chr12:29946074-29946075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11050434	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164948	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302346	0.93[AFR][1000 genomes]
rs67168837	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7303559	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305311	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312678	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv469191	chr12:29939628-30098770	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv557958	chr12:29939628-30098770	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv3413620	chr12:29942685-29948183	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
6	esv3447769	chr12:29942785-29948083	Weak transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
7	esv3337069	chr12:29942785-29948283	Weak transcription ZNF genes & repeats Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv557959	chr12:29944670-29959697	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7139255	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29943800-29946800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
2	chr12:29943800-29947200	ZNF genes & repeats	Fetal Kidney	kidney
3	chr12:29944000-29946800	Enhancers	Pancreas	Pancrea
4	chr12:29944000-29947000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr12:29944000-29947000	ZNF genes & repeats	Dnd41	blood
6	chr12:29944000-29947200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:29944000-29947200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:29944000-29947200	ZNF genes & repeats	Fetal Lung	lung
9	chr12:29944000-29947200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr12:29944200-29947200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
11	chr12:29944400-29946600	ZNF genes & repeats	Esophagus	oesophagus
12	chr12:29944800-29947000	ZNF genes & repeats	A549	lung
13	chr12:29945000-29947000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr12:29945400-29947000	ZNF genes & repeats	GM12878-XiMat	blood
15	chr12:29945600-29947000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:29946000-29947000	Weak transcription	Spleen	Spleen

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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