Variant report

Variant	rs12666897
Chromosome Location	chr7:103326194-103326195
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1012064	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs1012065	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs10487166	0.86[JPT][hapmap]
rs12705140	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705149	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12705150	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17154114	0.87[JPT][hapmap]
rs2017179	0.80[GIH][hapmap]
rs2240965	0.90[ASW][hapmap]
rs2299358	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs3808021	0.84[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs563264	0.89[LWK][hapmap]

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	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831085	chr7:103140672-103342388	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	esv1835816	chr7:103255144-103354223	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12666897	FLJ36031	cis	cerebellum	SCAN
rs12666897	TRIP6	cis	cerebellum	SCAN
rs12666897	RINT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103321400-103329800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:103321800-103330800	Weak transcription	K562	blood
3	chr7:103322200-103328800	Weak transcription	HepG2	liver
4	chr7:103326000-103331600	Enhancers	Brain Germinal Matrix	brain

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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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