Variant report

Variant	rs505780
Chromosome Location	chr3:59790427-59790428
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11720016	0.95[ASN][1000 genomes]
rs12494457	0.97[ASN][1000 genomes]
rs12634148	1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs13434180	0.97[ASN][1000 genomes]
rs2251216	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2629877	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs3100803	0.95[ASN][1000 genomes]
rs3112505	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4679507	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs497767	0.92[ASN][1000 genomes]
rs534185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs590581	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs591947	0.94[ASN][1000 genomes]
rs605545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6781354	0.86[CEU][hapmap]
rs9846213	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[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	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
6	nsv460563	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv590383	chr3:59772342-59827390	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59769800-59791400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr3:59770400-59825200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:59777200-59790800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:59778200-59811200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:59782400-59794800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:59787000-59795800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:59787200-59791000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:59787200-59802000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:59788400-59797600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:59788800-59795400	Weak transcription	Dnd41	blood
11	chr3:59789400-59795000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:59789400-59796800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:59789400-59797600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:59789400-59797600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:59789800-59794000	Weak transcription	Fetal Thymus	thymus
16	chr3:59789800-59797800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:59789800-59798000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:59790400-59790800	Enhancers	Placenta Amnion	Placenta Amnion

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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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