Variant report

Variant	rs12124665
Chromosome Location	chr1:85681538-85681539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11161555	0.96[ASN][1000 genomes]
rs11161557	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11161558	0.96[ASN][1000 genomes]
rs11161560	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11161563	0.89[JPT][hapmap]
rs12037869	0.86[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12117219	0.92[MEX][hapmap]
rs12406129	0.93[ASN][1000 genomes]
rs2185485	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9433250	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12124665	CLCA1	cis	cerebellum	SCAN
rs12124665	PKN2	cis	parietal	SCAN
rs12124665	CLCA3P	cis	cerebellum	SCAN
rs12124665	SPAG6	trans	lymphoblastoid	seeQTL
rs12124665	DDAH1	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85668000-85689000	Weak transcription	Gastric	stomach
2	chr1:85673800-85690400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:85679800-85682000	Enhancers	HepG2	liver
4	chr1:85680800-85681800	Enhancers	K562	blood
5	chr1:85681000-85681800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:85681200-85681600	Enhancers	Colon Smooth Muscle	Colon
7	chr1:85681400-85684400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:85681400-85686600	Weak transcription	Stomach Mucosa	stomach
9	chr1:85681400-85690400	Weak transcription	Stomach Smooth Muscle	stomach

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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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