Variant report

Variant	rs1485717
Chromosome Location	chr3:59766332-59766333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11130731	0.81[EUR][1000 genomes]
rs11707726	0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12486936	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12486972	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs12490126	0.86[EUR][1000 genomes]
rs13085067	0.84[EUR][1000 genomes]
rs13085511	0.84[EUR][1000 genomes]
rs13092167	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1485734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17061197	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs17361653	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34787563	0.88[ASN][1000 genomes]
rs35595242	0.87[ASN][1000 genomes]
rs4679505	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679608	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs492836	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs517644	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs550626	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55799227	0.95[ASN][1000 genomes]
rs56377327	0.95[ASN][1000 genomes]
rs575614	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs659193	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7616694	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs780365	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs780370	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs810525	0.99[ASN][1000 genomes]
rs972795	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813727	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9817691	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv1003387	chr3:59756364-59831340	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv460562	chr3:59760118-59826778	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv590381	chr3:59760118-59826778	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv590382	chr3:59763809-59793062	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59760400-59776000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:59761000-59772400	Weak transcription	Fetal Brain Male	brain
3	chr3:59761200-59768200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:59762000-59770000	Weak transcription	Fetal Thymus	thymus
5	chr3:59762400-59769600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:59763400-59769400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:59763600-59768800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:59764200-59769400	Weak transcription	GM12878-XiMat	blood
9	chr3:59764200-59770000	Weak transcription	Primary T cells from cord blood	blood
10	chr3:59764400-59769600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:59764600-59767000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:59764600-59769400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:59765200-59769200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:59765200-59769600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:59765400-59767800	Strong transcription	Dnd41	blood
16	chr3:59765600-59770000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:59765800-59769600	Weak transcription	Thymus	Thymus
18	chr3:59766000-59766400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:59766200-59766400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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