Variant report

Variant	rs2594247
Chromosome Location	chr3:60426592-60426593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1357320	0.83[YRI][hapmap]
rs17063156	0.86[YRI][hapmap]
rs17063250	1.00[AMR][1000 genomes]
rs2594249	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594251	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2594252	0.88[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2611414	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs2611415	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2611416	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs2611417	1.00[MEX][hapmap]
rs2687151	1.00[MEX][hapmap]
rs2687152	1.00[MEX][hapmap]
rs2687156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2687157	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2687158	0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2687163	1.00[MEX][hapmap]
rs2687189	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs2734373	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2734379	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56850618	0.81[AMR][1000 genomes]
rs57865322	1.00[AMR][1000 genomes]
rs58285270	0.81[AMR][1000 genomes]
rs59512348	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59642367	1.00[AMR][1000 genomes]
rs72876885	0.81[AMR][1000 genomes]
rs72876886	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72880359	1.00[AMR][1000 genomes]
rs7373797	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73833907	1.00[AMR][1000 genomes]
rs7623812	0.81[AMR][1000 genomes]
rs7632784	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7642636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877074	0.91[YRI][hapmap]

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	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
4	nsv590396	chr3:60330356-60447990	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv997531	chr3:60340440-60504992	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1010314	chr3:60367530-60459926	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv590397	chr3:60367607-60458976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv876849	chr3:60372144-60432292	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv876850	chr3:60379450-60426592	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv590398	chr3:60385765-60458976	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1013687	chr3:60388277-60458608	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1008235	chr3:60388277-60558331	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv460569	chr3:60388322-60558331	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv590399	chr3:60388322-60558331	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv2763271	chr3:60391557-60558331	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv999284	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv1002453	chr3:60391557-60558331	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv948513	chr3:60391557-60558331	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1008661	chr3:60397271-60558331	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv1005085	chr3:60397612-60532440	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv876851	chr3:60399322-60447990	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv876852	chr3:60399322-60458838	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv590400	chr3:60405004-60447369	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv1007745	chr3:60414407-60434882	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv460570	chr3:60418362-60465139	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv590401	chr3:60418362-60465139	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv876853	chr3:60420665-60512889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv1010907	chr3:60425237-60557503	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv1002978	chr3:60425237-60558331	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60420400-60430600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:60426400-60427000	Enhancers	Primary T helper cells fromperipheralblood	blood

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