Variant report

Variant	rs17680697
Chromosome Location	chr3:60759742-60759743
allele	C/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:15)

rs_ID	r²[population]
rs1014856	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12489644	0.94[ASN][1000 genomes]
rs12491786	0.92[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.98[ASN][1000 genomes]
rs12492010	0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12492901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1447927	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs17063990	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs35746862	0.83[EUR][1000 genomes]
rs4974228	1.00[CEU][hapmap];0.92[TSI][hapmap];0.99[EUR][1000 genomes]
rs4974241	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs56129149	0.90[ASN][1000 genomes]
rs56228932	0.90[ASN][1000 genomes]
rs6791644	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6794160	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs73836148	0.83[EUR][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	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv998815	chr3:60495872-60830769	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv999828	chr3:60537384-60785274	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17680697	FHIT	cis	parietal	SCAN
rs17680697	THOC7	cis	cerebellum	SCAN
rs17680697	SYNPR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60758800-60760400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:60758800-60761000	Weak transcription	Placenta	Placenta
3	chr3:60758800-60761800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:60758800-60761800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:60759000-60760200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:60759400-60762800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:60759600-60759800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:60759600-60760400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:60759600-60760400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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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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