Variant report

Variant	rs1996829
Chromosome Location	chr3:60416413-60416414
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1546817	0.95[CEU][hapmap]
rs1947161	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1996828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121861	0.81[EUR][1000 genomes]
rs2121862	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs2121863	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs2166824	0.85[CEU][hapmap]
rs241687	0.85[ASN][1000 genomes]
rs241688	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2594248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2594250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2687192	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687193	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2687194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2734375	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2734376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2734377	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2734387	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2734389	0.86[JPT][hapmap]
rs2734390	0.95[JPT][hapmap]
rs368926	0.91[CHB][hapmap]
rs378022	0.89[CHB][hapmap]
rs3856654	0.95[JPT][hapmap]
rs390523	0.91[CHB][hapmap]
rs391770	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs398105	0.91[CHB][hapmap]
rs400475	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs400747	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs410552	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs411734	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4234288	0.95[CEU][hapmap]
rs425036	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs439087	0.82[CHB][hapmap]
rs440692	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs4426639	0.80[ASN][1000 genomes]
rs452392	0.81[CEU][hapmap]
rs4638920	0.95[JPT][hapmap]
rs4679478	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs473944	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs478899	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs492530	0.86[ASN][1000 genomes]
rs59765327	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7645058	0.90[CEU][hapmap]
rs885737	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9826530	0.90[CEU][hapmap]
rs9846621	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9852001	0.85[CEU][hapmap]
rs9856092	0.90[CEU][hapmap]
rs9868373	0.95[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:33 , 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	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
5	nsv1011408	chr3:60307954-60417143	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1011133	chr3:60309541-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv519353	chr3:60310790-60417103	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv460568	chr3:60310790-60417103	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv590395	chr3:60310790-60417103	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1013291	chr3:60312356-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv876848	chr3:60367607-60420665	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	nsv1012953	chr3:60386782-60423266	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	nsv876851	chr3:60399322-60447990	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv876852	chr3:60399322-60458838	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv590400	chr3:60405004-60447369	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv1007745	chr3:60414407-60434882	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60415000-60417600	Enhancers	Primary T cells from cord blood	blood
2	chr3:60415200-60417200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:60415200-60417800	Enhancers	Fetal Thymus	thymus
4	chr3:60415600-60416600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:60415600-60416800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:60415600-60417600	Enhancers	Thymus	Thymus
7	chr3:60415800-60416800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:60416400-60417600	Enhancers	Fetal Heart	heart
9	chr3:60416400-60417800	Enhancers	K562	blood

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