Variant report

Variant	rs3821481
Chromosome Location	chr3:59971777-59971778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10490808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130742	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130743	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630463	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13061330	0.94[ASN][1000 genomes]
rs13061337	0.82[EUR][1000 genomes]
rs13063413	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13070349	0.88[ASN][1000 genomes]
rs13070475	0.93[ASN][1000 genomes]
rs13073897	0.84[EUR][1000 genomes]
rs13077692	0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs13081936	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13081972	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088505	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088669	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13092173	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13092997	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13094437	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13096138	0.95[CEU][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs212014	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2687899	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2736791	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3772458	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3772464	0.83[CHD][hapmap]
rs3772468	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772473	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772484	0.94[ASN][1000 genomes]
rs3772491	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772492	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772497	0.81[GIH][hapmap]
rs3772499	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772500	1.00[CEU][hapmap];0.81[GIH][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772502	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772505	0.91[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs3821478	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821479	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821480	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3821482	0.99[ASN][1000 genomes]
rs4679625	0.81[EUR][1000 genomes]
rs6446101	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6771484	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771698	0.94[ASN][1000 genomes]
rs6784057	0.87[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs6805337	0.93[ASN][1000 genomes]
rs7615116	0.80[ASN][1000 genomes]
rs7640107	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs802772	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs802774	0.88[ASN][1000 genomes]
rs812445	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv965380	chr3:59970574-59976399	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases
7	esv3419324	chr3:59971462-59973660	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases
8	esv3340378	chr3:59971537-59974085	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59965600-59974600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:59967400-59974400	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:59968000-59986600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:59968400-59971800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:59968400-59982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:59970000-59971800	Genic enhancers	Primary T cells from cord blood	blood
8	chr3:59970000-59972000	ZNF genes & repeats	Dnd41	blood
9	chr3:59970600-59972000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:59971000-59971800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr3:59971000-59972000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr3:59971000-59972200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:59971400-59972000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:59971400-59972200	Enhancers	Primary B cells from cord blood	blood
15	chr3:59971400-59972200	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:59971400-59972200	Enhancers	Thymus	Thymus
17	chr3:59971600-59971800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr3:59971600-59972000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:59971600-59972000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:59971600-59972000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:59971600-59972000	Enhancers	GM12878-XiMat	blood
22	chr3:59971600-59972000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:59971600-59972200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr3:59971600-59972200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:59971600-59972200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:59971600-59972200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:59971600-59974200	Weak transcription	Fetal Thymus	thymus

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