Variant report

Variant	rs2240461
Chromosome Location	chr6:87993090-87993091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13194868	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1328477	1.00[ASW][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs2274582	0.83[EUR][1000 genomes]
rs2325046	0.89[ASN][1000 genomes]
rs2875533	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4706290	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707349	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60992482	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7773715	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9294366	0.85[CEU][hapmap]
rs932742	0.86[ASW][hapmap];0.85[CEU][hapmap];0.86[TSI][hapmap]
rs9444485	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9450624	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9450659	0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752763	chr6:87981595-88001064	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2240461	C6orf162	cis	parietal	SCAN
rs2240461	MDN1	cis	parietal	SCAN
rs2240461	Hs.485895	cis	multi-tissue	Pritchard
rs2240461	C6orf162	Cis_1M	lymphoblastoid	RTeQTL
rs2240461	SLC35A1	cis	lymphoblastoid	seeQTL
rs2240461	C6orf162	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87970600-87994800	Weak transcription	Fetal Brain Female	brain
2	chr6:87991400-87993400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:87992000-87993200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:87992000-87993600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:87992800-87993200	Weak transcription	HMEC	breast
6	chr6:87993000-87993400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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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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