Variant report

Variant	rs995628
Chromosome Location	chr12:29239505-29239506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10843311	0.93[ASN][1000 genomes]
rs10843312	0.82[ASN][1000 genomes]
rs11050019	0.93[ASN][1000 genomes]
rs12422828	0.93[ASN][1000 genomes]
rs1390540	0.93[ASN][1000 genomes]
rs1496217	0.93[ASN][1000 genomes]
rs1496219	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1603382	0.93[ASN][1000 genomes]
rs1603384	0.93[ASN][1000 genomes]
rs1865764	0.80[AFR][1000 genomes]
rs2164493	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs4244845	0.93[ASN][1000 genomes]
rs4930849	0.80[AFR][1000 genomes]
rs4931144	0.93[ASN][1000 genomes]
rs4931145	0.93[ASN][1000 genomes]
rs4931146	0.93[ASN][1000 genomes]
rs4931147	0.93[ASN][1000 genomes]
rs4931148	0.93[ASN][1000 genomes]
rs6487757	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs7304088	0.80[AFR][1000 genomes]
rs7314861	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966290	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs7966398	0.88[YRI][hapmap]
rs7976074	0.93[ASN][1000 genomes]
rs995603	0.94[ASN][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2758301	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759888	chr12:29110782-29289849	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs995628	TMTC1	cis	parietal	SCAN
rs995628	TSPAN11	cis	parietal	SCAN
rs995628	ERGIC2	cis	cerebellum	SCAN
rs995628	IFLTD1	cis	parietal	SCAN
rs995628	MED21	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29239400-29239800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:29239400-29239800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr12:29239400-29240400	Enhancers	GM12878-XiMat	blood

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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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