Variant report

Variant	rs2588395
Chromosome Location	chr12:40900137-40900138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10878602	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10878603	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11176655	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11564230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581232	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388782	0.94[ASN][1000 genomes]
rs1388784	0.92[ASN][1000 genomes]
rs1427259	0.84[JPT][hapmap]
rs1427261	0.84[JPT][hapmap];0.87[MEX][hapmap]
rs1444215	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1492321	0.81[TSI][hapmap]
rs1816207	0.84[JPT][hapmap]
rs2588414	0.94[ASN][1000 genomes]
rs2588417	0.93[ASN][1000 genomes]
rs2638866	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638868	0.93[ASN][1000 genomes]
rs2638876	0.81[ASN][1000 genomes]
rs2638877	0.88[ASN][1000 genomes]
rs2638881	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920813	0.94[ASN][1000 genomes]
rs2920832	0.94[ASN][1000 genomes]
rs2933346	0.92[ASN][1000 genomes]
rs2933353	0.92[ASN][1000 genomes]
rs2933354	0.94[ASN][1000 genomes]
rs2933364	0.94[ASN][1000 genomes]
rs2933379	0.92[ASN][1000 genomes]
rs2933380	0.92[ASN][1000 genomes]
rs3861083	0.84[JPT][hapmap]
rs4099579	0.84[JPT][hapmap]
rs6581723	0.84[JPT][hapmap];0.94[MEX][hapmap]
rs7136122	0.84[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	esv3519672	chr12:40898422-40907859	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv983435	chr12:40898783-40903918	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3377041	chr12:40898929-40905079	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv9377	chr12:40898931-40905123	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3387261	chr12:40898980-40905120	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3519673	chr12:40898984-40905196	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3519675	chr12:40898984-40905196	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv512268	chr12:40899000-40905722	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3402193	chr12:40899025-40905131	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3431848	chr12:40899046-40902055	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	esv3447251	chr12:40899046-40905008	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3524253	chr12:40899064-40905070	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3524254	chr12:40899064-40905070	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3349674	chr12:40899126-40905088	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3446930	chr12:40899146-40905058	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv3325479	chr12:40899796-40902880	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3417437	chr12:40900070-40907460	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2588395	SLC2A13	cis	cerebellum	SCAN
rs2588395	ZCRB1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40894800-40908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40899200-40904600	Weak transcription	GM12878-XiMat	blood

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