Variant report

Variant	rs2620340
Chromosome Location	chr12:122291261-122291262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122284827..122287337-chr12:122291001..122292909,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10840626	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840627	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11043222	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11043226	0.85[AMR][1000 genomes]
rs11502392	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1154510	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1154515	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11614623	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1169077	0.82[CEU][hapmap]
rs1169085	0.82[CEU][hapmap]
rs1169093	0.82[CEU][hapmap]
rs1182927	0.82[CEU][hapmap]
rs1185260	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs1667580	0.81[EUR][1000 genomes]
rs1667583	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs1678967	0.85[AMR][1000 genomes]
rs1678969	0.84[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1720041	0.82[CEU][hapmap]
rs1720067	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1795967	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1947826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2101017	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2230681	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2247139	0.81[EUR][1000 genomes]
rs2247291	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2309274	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2596137	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2596144	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2620332	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688412	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2707056	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4760099	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs493519	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs6486794	0.82[CEU][hapmap]
rs7314056	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7957207	0.91[CEU][hapmap]
rs7961103	0.91[CEU][hapmap]
rs830122	0.82[CEU][hapmap]
rs830124	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap]
rs853758	1.00[CEU][hapmap]
rs895958	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs895959	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9668191	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3420303	chr12:122287669-122291867	Weak transcription Flanking Active TSS Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2620340	SETD1B	cis	parietal	SCAN
rs2620340	RNF10	cis	cerebellum	SCAN
rs2620340	CCDC62	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122278200-122294000	Weak transcription	Spleen	Spleen
2	chr12:122278200-122296400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:122278400-122293000	Weak transcription	GM12878-XiMat	blood
4	chr12:122278400-122295400	Weak transcription	Fetal Intestine Small	intestine
5	chr12:122281400-122292600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:122287600-122292400	Weak transcription	HepG2	liver
7	chr12:122287800-122292200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:122288200-122292600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:122288400-122292600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr12:122288800-122292600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:122290000-122292000	Strong transcription	Liver	Liver
12	chr12:122291200-122295400	Weak transcription	Pancreas	Pancrea

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