Variant report

Variant	rs7312678
Chromosome Location	chr12:29947081-29947082
allele	A/C
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	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164948	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs302346	0.84[AFR][1000 genomes]
rs67168837	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7139255	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7303559	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7305311	0.89[AFR][1000 genomes];0.96[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
rs7312678	TMTC1	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29943800-29947200	ZNF genes & repeats	Fetal Kidney	kidney
2	chr12:29944000-29947200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:29944000-29947200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:29944000-29947200	ZNF genes & repeats	Fetal Lung	lung
5	chr12:29944000-29947200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr12:29944200-29947200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
7	chr12:29946400-29953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:29946600-29947200	Active TSS	Fetal Brain Male	brain
9	chr12:29946800-29947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:29947000-29947200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:29947000-29947200	Enhancers	Esophagus	oesophagus
12	chr12:29947000-29947200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr12:29947000-29947200	ZNF genes & repeats	Spleen	Spleen
14	chr12:29947000-29947200	Enhancers	NHDF-Ad	bronchial
15	chr12:29947000-29947600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:29947000-29948200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:29947000-29948600	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:29947000-29950800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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Input of quick search could be:

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

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