Variant report

Variant	rs12696110
Chromosome Location	chr3:160641930-160641931
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160641537..160644034-chr3:161124044..161126884,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10513558	0.86[JPT][hapmap]
rs11709802	0.92[JPT][hapmap]
rs12485723	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12494673	0.86[JPT][hapmap]
rs12634368	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13325518	0.85[GIH][hapmap]
rs1348977	0.80[CHD][hapmap];0.93[JPT][hapmap]
rs1374795	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs1447608	0.86[JPT][hapmap]
rs1447617	0.92[JPT][hapmap]
rs1447624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1839014	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1839018	0.85[GIH][hapmap]
rs1868104	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs1868106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028988	0.93[JPT][hapmap];0.82[TSI][hapmap]
rs2121721	0.85[JPT][hapmap]
rs4679667	1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6441334	0.93[JPT][hapmap]
rs6441335	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6441336	0.93[JPT][hapmap]
rs6770488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6789195	0.93[JPT][hapmap]
rs6796612	0.98[EUR][1000 genomes]
rs6797498	0.93[JPT][hapmap]
rs6799391	0.93[JPT][hapmap]
rs6800092	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610732	0.93[JPT][hapmap]
rs7629374	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs778655	0.85[JPT][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12696110	C3orf57	cis	parietal	SCAN
rs12696110	C3orf57	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160635400-160644000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:160635400-160649200	Weak transcription	Fetal Brain Female	brain
3	chr3:160636000-160644000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:160638200-160647200	Weak transcription	Right Ventricle	heart
5	chr3:160638400-160643800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:160638400-160643800	Weak transcription	Right Atrium	heart
7	chr3:160639000-160644400	Weak transcription	Fetal Brain Male	brain
8	chr3:160641600-160642000	Weak transcription	Psoas Muscle	Psoas
9	chr3:160641800-160642200	Enhancers	Left Ventricle	heart

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