Variant report

Variant	rs1439008
Chromosome Location	chr3:61066987-61066988
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11711708	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11712505	1.00[JPT][hapmap]
rs13095410	1.00[JPT][hapmap]
rs13095530	1.00[JPT][hapmap]
rs1347852	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs1439005	0.93[JPT][hapmap]
rs1439006	0.87[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1439007	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1595603	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1898752	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2083264	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2165044	1.00[JPT][hapmap]
rs2365057	0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs6445190	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445191	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445192	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6445194	0.93[JPT][hapmap]
rs6764497	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap]
rs6774194	0.93[JPT][hapmap]
rs7610484	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7626688	0.93[JPT][hapmap]
rs7649991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7650309	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7651431	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9820971	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9825823	0.84[CHD][hapmap];0.93[JPT][hapmap]
rs9830950	0.93[JPT][hapmap]
rs9845837	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876864	chr3:60952040-61103609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv915904	chr3:60952040-61125194	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1012510	chr3:60952040-61131709	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536578	chr3:60952040-61131709	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv834710	chr3:60995631-61148157	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv2756993	chr3:61064432-61119923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	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	chr3:61063000-61067400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr3:61063800-61067000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:61065200-61067600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:61065200-61067800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:61065800-61067200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:61065800-61067400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:61065800-61067600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:61066000-61067200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:61066000-61067400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr3:61066200-61067000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:61066400-61067000	Enhancers	Brain Hippocampus Middle	brain
12	chr3:61066400-61067200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:61066400-61067400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:61066400-61067600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:61066600-61067000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:61066600-61067000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:61066600-61067000	Active TSS	Brain Anterior Caudate	brain
18	chr3:61066600-61067200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr3:61066600-61067400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:61066600-61067400	Enhancers	Brain Angular Gyrus	brain
21	chr3:61066600-61067400	Enhancers	Brain Substantia Nigra	brain
22	chr3:61066600-61067600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:61066600-61067600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr3:61066800-61067000	Enhancers	Brain Cingulate Gyrus	brain
25	chr3:61066800-61067200	Enhancers	NHEK	skin
26	chr3:61066800-61067400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:61066800-61067400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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