Variant report

Variant	rs790474
Chromosome Location	chr5:127151003-127151004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs245184	0.85[ASN][1000 genomes]
rs245185	1.00[JPT][hapmap]
rs711359	1.00[ASN][1000 genomes]
rs790476	0.86[ASN][1000 genomes]
rs790477	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1021483	chr5:126927834-127304873	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs790474	HINT1	cis	cerebellum	SCAN
rs790474	SEPW1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127139200-127151800	Weak transcription	Stomach Mucosa	stomach
2	chr5:127148000-127151200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:127148000-127151200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:127148000-127151200	Enhancers	Rectal Smooth Muscle	rectum
5	chr5:127148400-127152400	Enhancers	Fetal Stomach	stomach
6	chr5:127148800-127151400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:127149000-127154400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:127149200-127151200	Enhancers	Ovary	ovary
9	chr5:127149800-127152000	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr5:127150000-127159400	Weak transcription	Right Atrium	heart
11	chr5:127150400-127151400	Enhancers	Colon Smooth Muscle	Colon
12	chr5:127150400-127152000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:127150400-127154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:127151000-127151200	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr5:127151000-127154200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:127151000-127156600	Weak transcription	NHDF-Ad	bronchial
17	chr5:127151000-127159000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:127151000-127161200	Weak transcription	HSMM	muscle

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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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