Variant report

Variant	rs1439007
Chromosome Location	chr3:61066925-61066926
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11711708	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712505	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13066447	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13095410	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13095530	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1347852	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1439005	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1439008	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1554601	0.81[JPT][hapmap]
rs1898752	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2083264	0.83[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs2165044	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2365057	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs35555910	0.81[AMR][1000 genomes]
rs6445190	0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs6445191	0.84[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs6445192	0.84[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs6445194	1.00[JPT][hapmap]
rs6764497	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs6774194	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs7611232	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7626688	1.00[JPT][hapmap]
rs7645096	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7649991	0.88[ASN][1000 genomes]
rs7650309	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7651431	0.88[ASN][1000 genomes]
rs9820971	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs9825823	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs9830950	1.00[JPT][hapmap]
rs9845837	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links