Variant report

Variant	rs262340
Chromosome Location	chr7:103418242-103418243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10251365	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10255733	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10280683	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11496125	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1510845	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1510846	1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs17155888	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2237637	0.95[GIH][hapmap];0.88[TSI][hapmap]
rs2299381	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2299383	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2299386	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs262339	1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28557041	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39328	0.82[JPT][hapmap]
rs886804	1.00[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.80[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	nsv427799	chr7:103250733-103454202	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1016328	chr7:103396911-103443565	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv539048	chr7:103396911-103443565	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs262340	TSC22D4	cis	cerebellum	SCAN
rs262340	POLR2J	cis	parietal	SCAN
rs262340	COPS6	cis	cerebellum	SCAN
rs262340	C7orf52	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103390000-103434000	Weak transcription	K562	blood
2	chr7:103406000-103433600	Weak transcription	HepG2	liver
3	chr7:103418000-103418400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr7:103418000-103418400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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