Variant report

Variant	rs2472682
Chromosome Location	chr3:119532652-119532653
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119531732..119533815-chr3:119534255..119536418,2	MCF-7	breast:
2	chr3:119041713..119043287-chr3:119530571..119533210,2	MCF-7	breast:
3	chr3:119530112..119533112-chr3:119811901..119815932,5	MCF-7	breast:
4	chr3:119532575..119535119-chr3:119538231..119540719,2	K562	blood:
5	chr3:119532575..119536291-chr3:119538231..119540719,3	K562	blood:
6	chr3:119531331..119533784-chr3:119534969..119537956,2	K562	blood:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13321783	0.91[CEU][hapmap]
rs1546753	0.83[AMR][1000 genomes]
rs1719890	0.84[AMR][1000 genomes]
rs1719894	0.91[CEU][hapmap];0.81[MEX][hapmap];0.85[AMR][1000 genomes]
rs1732168	0.86[AMR][1000 genomes]
rs1732170	0.91[CEU][hapmap];0.84[AMR][1000 genomes]
rs2319398	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs2319399	0.91[CEU][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs28536662	0.91[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes]
rs3107669	0.91[CEU][hapmap]
rs3732361	0.91[CEU][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs4261913	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs4491945	0.86[AMR][1000 genomes]
rs57695730	0.84[AMR][1000 genomes]
rs58605236	0.84[AMR][1000 genomes]
rs6438552	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs6438553	0.90[CEU][hapmap];0.86[AMR][1000 genomes]
rs6782799	0.91[CEU][hapmap];0.85[AMR][1000 genomes]
rs6784598	0.91[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6785049	0.91[CEU][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6792572	0.91[CEU][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs6795653	0.91[CEU][hapmap];0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs6800622	0.91[CEU][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes]
rs6805251	0.90[CEU][hapmap];0.83[AMR][1000 genomes]
rs6808975	0.85[AMR][1000 genomes]
rs7611736	0.85[AMR][1000 genomes]
rs7644234	0.91[CEU][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes]
rs9813864	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs9866394	0.83[AMR][1000 genomes]
rs9873477	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes]
rs9878473	0.91[CEU][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs9879295	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2472682	MUC13	cis	parietal	SCAN
rs2472682	GTF2E1	cis	parietal	SCAN
rs2472682	GSK3B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119516800-119534600	Weak transcription	HepG2	liver
2	chr3:119528200-119533800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:119529200-119533200	Strong transcription	Liver	Liver
4	chr3:119529400-119533600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:119529400-119533600	Weak transcription	Colonic Mucosa	Colon
6	chr3:119529400-119535800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:119529400-119537000	Strong transcription	Fetal Intestine Large	intestine
8	chr3:119529400-119537800	Strong transcription	Fetal Intestine Small	intestine
9	chr3:119529400-119544000	Weak transcription	Right Atrium	heart
10	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:119529600-119536000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:119529600-119543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
14	chr3:119529800-119543600	Weak transcription	GM12878-XiMat	blood
15	chr3:119530200-119542800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:119531400-119534600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:119531600-119536200	Weak transcription	Fetal Heart	heart
18	chr3:119532000-119543800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:119532200-119533600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:119532400-119535800	Weak transcription	Left Ventricle	heart
21	chr3:119532400-119551000	Weak transcription	Right Ventricle	heart

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