Variant report

Variant	rs12327673
Chromosome Location	chr19:36741104-36741105
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11882451	1.00[EUR][1000 genomes]
rs17885104	1.00[EUR][1000 genomes]
rs28396149	1.00[EUR][1000 genomes]
rs28812837	1.00[EUR][1000 genomes]
rs7248312	1.00[EUR][1000 genomes]
rs7248820	1.00[EUR][1000 genomes]
rs7249613	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12327673	SCT	trans	lymphoblastoid	seeQTL
rs12327673	ULK2	trans	lymphoblastoid	seeQTL
rs12327673	FOXG1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36730400-36748400	Weak transcription	HSMMtube	muscle
2	chr19:36736200-36746200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:36737400-36747800	Weak transcription	Brain Anterior Caudate	brain
4	chr19:36737400-36747800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:36737400-36748000	Weak transcription	Ovary	ovary
6	chr19:36737600-36745400	Weak transcription	Pancreas	Pancrea
7	chr19:36737600-36746000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:36737600-36746200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:36737600-36747800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:36737600-36747800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:36737600-36747800	Weak transcription	Brain Hippocampus Middle	brain
12	chr19:36738000-36747800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:36739200-36746200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:36739200-36746800	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:36739400-36745400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:36739600-36745200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:36739600-36756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr19:36740200-36743200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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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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