Variant report

Variant	rs9820238
Chromosome Location	chr3:60052007-60052008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10510827	0.82[JPT][hapmap]
rs125634	0.85[ASN][1000 genomes]
rs1496651	1.00[CEU][hapmap]
rs17062206	0.82[JPT][hapmap]
rs17062502	1.00[CEU][hapmap]
rs17062508	1.00[CEU][hapmap]
rs17062567	1.00[CEU][hapmap]
rs17062605	1.00[CEU][hapmap]
rs3856669	0.83[CHD][hapmap]
rs6776575	1.00[CEU][hapmap]
rs6788803	0.82[JPT][hapmap]
rs6801030	1.00[CEU][hapmap]
rs9311747	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs969561	0.82[JPT][hapmap]
rs9818696	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9819602	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9823026	0.82[CHB][hapmap]
rs9829623	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs9830224	1.00[CEU][hapmap]
rs9837820	1.00[CEU][hapmap]
rs9839754	1.00[CEU][hapmap]
rs9860502	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS 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	1 gene(s)	inside rSNPs	diseases
5	esv13593	chr3:60050980-60057155	Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60045000-60054200	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr3:60045800-60052400	Enhancers	Primary T cells from cord blood	blood
3	chr3:60047400-60052200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:60048200-60054000	Enhancers	Dnd41	blood
5	chr3:60048800-60059400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:60049400-60053200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:60049800-60052200	Enhancers	Fetal Thymus	thymus
8	chr3:60050800-60052400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:60051200-60052400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:60051600-60052400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:60051600-60053200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:60051600-60062000	Weak transcription	Aorta	Aorta
13	chr3:60051800-60056200	Weak transcription	Thymus	Thymus
14	chr3:60051800-60058200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:60051800-60063000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:60052000-60058400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:60052000-60059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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