Variant report

Variant	rs9827643
Chromosome Location	chr3:60213301-60213302
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10510833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10510834	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs13082004	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes]
rs1472369	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs17336290	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs17395220	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17395248	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17396765	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap]
rs17397398	0.90[EUR][1000 genomes]
rs1908771	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs213312	0.83[ASN][1000 genomes]
rs213315	0.82[JPT][hapmap]
rs213322	0.85[CHD][hapmap]
rs213388	0.82[CEU][hapmap]
rs34884909	0.95[EUR][1000 genomes]
rs35332698	0.90[EUR][1000 genomes]
rs4679647	0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4679648	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[TSI][hapmap]
rs6765672	0.86[ASN][1000 genomes]
rs6775757	0.93[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6784012	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6787176	0.88[ASN][1000 genomes]
rs6795591	1.00[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71313750	0.83[ASN][1000 genomes]
rs720285	0.89[CHB][hapmap];0.85[CHD][hapmap]
rs7628950	0.93[CEU][hapmap];0.94[CHB][hapmap]
rs9311754	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs9311755	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs9810084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819920	0.93[CEU][hapmap];0.92[GIH][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs9823838	0.96[ASN][1000 genomes]
rs9831415	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[TSI][hapmap]
rs9832192	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs9834515	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9857010	0.83[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs9870279	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv2752010	chr3:60067396-60288428	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1009063	chr3:60067866-60277128	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1013919	chr3:60067866-60284882	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv519855	chr3:60068730-60276722	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv460566	chr3:60068730-60276722	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv460567	chr3:60068730-60276722	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv590390	chr3:60068730-60276722	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv590391	chr3:60068730-60277709	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1008586	chr3:60070974-60258108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv536576	chr3:60070974-60258108	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1008267	chr3:60071947-60264461	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1007798	chr3:60071947-60277128	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv2763751	chr3:60071959-60292312	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2752011	chr3:60073153-60288428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv432421	chr3:60073153-60288428	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv915646	chr3:60088475-60240653	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1003632	chr3:60095363-60258108	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv536577	chr3:60095363-60258108	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1010969	chr3:60124962-60425297	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv1001270	chr3:60136017-60218582	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv834708	chr3:60156091-60305452	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv876841	chr3:60189471-60272317	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv2422232	chr3:60192201-60334555	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv876842	chr3:60196537-60233087	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv876843	chr3:60196537-60269948	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9827643	THOC7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60212400-60213400	Enhancers	Dnd41	blood

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