Variant report

Variant	rs4520446
Chromosome Location	chr1:97966205-97966206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10747483	0.85[ASN][1000 genomes]
rs10875093	0.93[ASN][1000 genomes]
rs10875095	0.93[ASN][1000 genomes]
rs11165882	0.94[CHB][hapmap];0.80[CHD][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs1337752	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2027250	0.93[ASN][1000 genomes]
rs2105129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2786512	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2786513	0.85[ASN][1000 genomes]
rs2786770	0.90[ASN][1000 genomes]
rs2786776	0.96[ASN][1000 genomes]
rs2786781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2786782	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2786784	0.93[ASN][1000 genomes]
rs2811172	0.88[ASN][1000 genomes]
rs2811173	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2811174	1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2811175	0.89[ASN][1000 genomes]
rs2811176	0.91[ASN][1000 genomes]
rs2811177	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2811178	0.82[ASN][1000 genomes]
rs2811182	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2811184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2811186	0.97[ASN][1000 genomes]
rs2811188	0.95[ASN][1000 genomes]
rs4364915	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs4427441	0.91[ASN][1000 genomes]
rs4950037	0.80[ASN][1000 genomes]
rs6679873	0.89[ASN][1000 genomes]
rs6687950	0.89[ASN][1000 genomes]
rs7529624	0.87[ASN][1000 genomes]
rs868184	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533039	chr1:97665736-98343102	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv530049	chr1:97883261-98384614	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv830703	chr1:97907708-98101144	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv519191	chr1:97945292-98000861	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv871449	chr1:97950034-97979317	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97872600-98014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:97928600-98018200	Weak transcription	Ovary	ovary
3	chr1:97930600-97979200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:97945200-97974200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:97945200-97976000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:97945400-97969600	Weak transcription	Primary T cells from cord blood	blood
7	chr1:97945600-97967000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:97955800-97966400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:97955800-97966400	Weak transcription	NHDF-Ad	bronchial
10	chr1:97955800-97990000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:97956400-98009400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:97959000-97974600	Weak transcription	Lung	lung
13	chr1:97963000-98009400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:97964600-98010400	Weak transcription	Dnd41	blood
15	chr1:97964800-97968200	Enhancers	Liver	Liver
16	chr1:97965000-97985200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:97965400-97966600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:97965400-97976000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:97965800-97975600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:97966000-97966600	Active TSS	Fetal Brain Male	brain
21	chr1:97966000-97966800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:97966000-97974400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:97966200-97966400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:97966200-97966400	Active TSS	Brain Hippocampus Middle	brain
25	chr1:97966200-97966600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:97966200-97966600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:97966200-97966600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:97966200-97966600	Active TSS	Brain Anterior Caudate	brain
29	chr1:97966200-97966600	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr1:97966200-97966600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:97966200-97966600	Enhancers	Fetal Heart	heart
32	chr1:97966200-97966600	Flanking Active TSS	Fetal Lung	lung
33	chr1:97966200-97966600	Active TSS	Right Atrium	heart
34	chr1:97966200-97966800	Enhancers	Brain Germinal Matrix	brain
35	chr1:97966200-97966800	Active TSS	Brain Substantia Nigra	brain
36	chr1:97966200-97970800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:97966200-97973800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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