Variant report

Variant	rs12690576
Chromosome Location	chr3:160647912-160647913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160646068..160648329-chr3:160652123..160654402,3	K562	blood:
2	chr3:160473266..160475652-chr3:160647072..160650166,3	MCF-7	breast:
3	chr3:160643537..160645831-chr3:160647633..160653129,5	MCF-7	breast:
4	chr3:160638572..160639554-chr3:160647137..160648004,3	MCF-7	breast:
5	chr3:160476666..160477325-chr3:160647136..160648071,2	MCF-7	breast:
6	chr3:160295180..160296212-chr3:160647263..160648035,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10513560	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs10936215	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13098529	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1345156	0.87[JPT][hapmap]
rs1374787	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs1447608	0.83[CEU][hapmap]
rs1447626	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs1530636	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs1562465	0.87[CEU][hapmap]
rs1580254	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs1868108	1.00[CEU][hapmap]
rs1868109	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2121721	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs2376476	0.82[EUR][1000 genomes]
rs2376477	0.83[EUR][1000 genomes]
rs4679663	0.83[EUR][1000 genomes]
rs4679928	0.82[EUR][1000 genomes]
rs6441345	0.80[TSI][hapmap]
rs6770180	0.82[CEU][hapmap]
rs6774203	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs6808386	0.84[CEU][hapmap]
rs733948	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs745707	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611005	0.82[EUR][1000 genomes]
rs7613316	0.83[CEU][hapmap]
rs7616249	0.84[CEU][hapmap]
rs7626904	0.82[EUR][1000 genomes]
rs7626985	0.82[EUR][1000 genomes]
rs7635796	0.84[CEU][hapmap]
rs7640874	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs7644586	0.84[CEU][hapmap]
rs956447	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9832109	0.86[GIH][hapmap]
rs9839984	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9846254	0.80[TSI][hapmap]
rs9857743	0.87[CEU][hapmap]
rs9858335	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs9860182	0.80[CEU][hapmap];0.80[TSI][hapmap]
rs9860537	0.87[JPT][hapmap]
rs9881807	1.00[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12690576	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs12690576	PPM1L	cis	cerebellum	SCAN
rs12690576	C3orf57	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160635400-160649200	Weak transcription	Fetal Brain Female	brain
2	chr3:160644800-160654400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:160645000-160648400	Weak transcription	Fetal Brain Male	brain
4	chr3:160646000-160648600	Enhancers	Left Ventricle	heart
5	chr3:160646000-160648600	Enhancers	Psoas Muscle	Psoas
6	chr3:160647000-160648000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:160647200-160648000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:160647200-160648000	Enhancers	Adipose Nuclei	Adipose
9	chr3:160647200-160648000	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr3:160647200-160648000	Enhancers	NHDF-Ad	bronchial
11	chr3:160647200-160650200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:160647400-160648000	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:160647600-160648600	Weak transcription	Fetal Heart	heart
14	chr3:160647600-160648600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:160647600-160649000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:160647600-160649000	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:160647600-160650400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:160647600-160652400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:160647800-160649000	Weak transcription	Brain Angular Gyrus	brain
20	chr3:160647800-160649200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:160647800-160649200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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