Variant report

Variant	rs6445198
Chromosome Location	chr3:61219865-61219866
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10866046	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130821	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130822	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130826	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130828	0.84[EUR][1000 genomes]
rs11130833	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11130834	0.99[ASN][1000 genomes]
rs11130835	0.99[ASN][1000 genomes]
rs11720254	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492551	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1470035	0.87[EUR][1000 genomes]
rs1524019	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1554599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17064630	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1916800	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1916801	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1916802	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs1949772	0.92[EUR][1000 genomes]
rs1980308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1980311	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2365389	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34515056	0.81[EUR][1000 genomes]
rs35198002	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4296587	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4535219	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs4605537	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688352	0.88[EUR][1000 genomes]
rs4688354	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4688355	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4688359	0.81[EUR][1000 genomes]
rs4688379	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6445197	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445199	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6445200	0.84[CEU][hapmap];0.94[EUR][1000 genomes]
rs6785875	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6787292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6787313	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6809031	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71296711	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432943	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7647122	0.84[EUR][1000 genomes]
rs815709	0.92[EUR][1000 genomes]
rs815710	0.91[EUR][1000 genomes]
rs815712	0.90[EUR][1000 genomes]
rs815715	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs815717	0.93[EUR][1000 genomes]
rs843812	0.92[EUR][1000 genomes]
rs863635	0.91[EUR][1000 genomes]
rs9831249	0.94[EUR][1000 genomes]
rs9832387	0.88[EUR][1000 genomes]
rs9832404	0.85[EUR][1000 genomes]
rs9843007	0.81[EUR][1000 genomes]
rs9844741	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs9846073	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9850114	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9855716	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs9856859	0.83[EUR][1000 genomes]
rs9857131	0.84[ASN][1000 genomes]
rs9859004	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860681	0.86[EUR][1000 genomes]
rs9875827	0.89[EUR][1000 genomes]
rs9882800	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS 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
6	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv997718	chr3:61176349-61222975	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61201200-61221000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61203200-61222200	Weak transcription	Psoas Muscle	Psoas
3	chr3:61203400-61225600	Weak transcription	Lung	lung
4	chr3:61203400-61225600	Weak transcription	Pancreas	Pancrea
5	chr3:61208000-61225600	Weak transcription	Right Atrium	heart
6	chr3:61212000-61222200	Weak transcription	Left Ventricle	heart
7	chr3:61213400-61222200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:61218000-61222200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:61218400-61220200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:61219200-61220200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:61219400-61220000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:61219400-61220000	Enhancers	Brain Hippocampus Middle	brain
13	chr3:61219400-61220000	Enhancers	Ovary	ovary
14	chr3:61219400-61220200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:61219400-61220200	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:61219400-61221000	Enhancers	GM12878-XiMat	blood
17	chr3:61219600-61220000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:61219800-61220000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:61219800-61220000	Enhancers	Brain Anterior Caudate	brain
20	chr3:61219800-61222000	Weak transcription	Small Intestine	intestine
21	chr3:61219800-61222200	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links