Variant report

Variant	rs990276
Chromosome Location	chr2:78542946-78542947
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10165699	0.88[CHB][hapmap]
rs10166502	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10172503	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10197523	0.88[CHB][hapmap]
rs10204484	0.94[CHB][hapmap]
rs10205850	0.92[CHB][hapmap]
rs10210902	0.88[CHB][hapmap]
rs1028148	0.80[AMR][1000 genomes]
rs1040179	0.88[CHB][hapmap]
rs10865434	0.94[CHB][hapmap]
rs11126672	0.88[CHB][hapmap]
rs1158017	0.93[CHB][hapmap]
rs12613066	0.88[CHB][hapmap]
rs13014178	0.94[CHB][hapmap]
rs13385712	0.88[CHB][hapmap]
rs1378427	0.94[CHB][hapmap]
rs1378428	0.89[CHB][hapmap]
rs1400133	0.88[CHB][hapmap]
rs1400134	0.88[CHB][hapmap]
rs1455384	0.88[CHB][hapmap]
rs1455385	0.88[CHB][hapmap]
rs1516251	0.88[CHB][hapmap]
rs1516253	0.94[CHB][hapmap]
rs1526388	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1543141	0.85[CHB][hapmap]
rs1545580	0.92[ASN][1000 genomes]
rs1563313	0.83[GIH][hapmap]
rs1563314	0.88[CHB][hapmap];0.82[AMR][1000 genomes]
rs1568062	0.88[CHB][hapmap]
rs1606996	0.81[AMR][1000 genomes]
rs2018108	0.94[CHB][hapmap];0.80[AMR][1000 genomes]
rs2138488	0.88[CHB][hapmap]
rs2203582	0.88[CHB][hapmap]
rs2219183	0.94[CHB][hapmap]
rs2861611	0.94[CHB][hapmap]
rs2861613	0.88[CHB][hapmap]
rs4303736	0.94[CHB][hapmap]
rs4853388	0.87[CHB][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes]
rs4853394	0.88[CHB][hapmap]
rs6547196	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6717285	0.88[CHB][hapmap]
rs6725891	0.94[CHB][hapmap];0.81[AMR][1000 genomes]
rs6742566	0.90[ASN][1000 genomes]
rs7580922	0.94[CHB][hapmap]
rs768071	0.94[CHB][hapmap];0.87[GIH][hapmap]
rs908439	0.88[CHB][hapmap];0.87[GIH][hapmap]
rs932141	0.94[CHB][hapmap]
rs941019	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917204	chr2:78047538-78602013	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1001461	chr2:78091352-78673948	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757811	chr2:78126389-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759068	chr2:78126389-78711032	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2756933	chr2:78199735-78640246	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv524102	chr2:78221253-78562013	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2762686	chr2:78224683-78564328	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv34528	chr2:78256829-78615143	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv818057	chr2:78263883-78633880	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1005115	chr2:78307330-78673948	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1002464	chr2:78308336-78658280	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv535787	chr2:78308336-78658280	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv582270	chr2:78367077-78592167	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv1011578	chr2:78368127-78590333	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv874357	chr2:78395467-78546919	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv1010116	chr2:78399683-78660165	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv998161	chr2:78404349-78660165	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv1000078	chr2:78410008-78660165	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv428710	chr2:78451500-78602039	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv1002114	chr2:78511306-78743191	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv535789	chr2:78511306-78743191	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv834271	chr2:78519702-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs990276	DQX1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78536600-78544800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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