Variant report

Variant	rs6479596
Chromosome Location	chr9:97830169-97830170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97822176..97825096-chr9:97827855..97830416,5	MCF-7	breast:
2	chr9:97682234..97685097-chr9:97826323..97831388,4	MCF-7	breast:
3	chr9:97829667..97831442-chr9:97833759..97836647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1020962	0.91[EUR][1000 genomes]
rs1038092	0.91[EUR][1000 genomes]
rs10761371	1.00[EUR][1000 genomes]
rs10993471	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12683030	0.88[JPT][hapmap]
rs1564235	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1571896	0.87[EUR][1000 genomes]
rs1571897	0.87[ASN][1000 genomes]
rs1699499	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1871220	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1888944	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1888945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1888946	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061798	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061799	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061801	0.91[EUR][1000 genomes]
rs3739748	0.87[EUR][1000 genomes]
rs3802449	0.88[JPT][hapmap]
rs400727	0.88[JPT][hapmap]
rs4647549	0.86[JPT][hapmap]
rs4743975	0.87[EUR][1000 genomes]
rs4743976	0.87[ASN][1000 genomes]
rs4743977	0.91[EUR][1000 genomes]
rs4743978	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744421	0.87[EUR][1000 genomes]
rs6479597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7039768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97818800-97830400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
4	chr9:97820400-97840800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:97820400-97843000	Weak transcription	Primary T cells from cord blood	blood
6	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr9:97821000-97838400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:97821200-97839000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:97821200-97839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:97821400-97843200	Weak transcription	Fetal Brain Female	brain
11	chr9:97821800-97835600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:97822000-97834600	Strong transcription	Hela-S3	cervix
13	chr9:97822200-97833200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr9:97822800-97830200	Genic enhancers	Left Ventricle	heart
15	chr9:97822800-97831600	Genic enhancers	Muscle Satellite Cultured Cells	--
16	chr9:97822800-97832800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
17	chr9:97822800-97845400	Weak transcription	Primary B cells from cord blood	blood
18	chr9:97823600-97834600	Strong transcription	NH-A	brain
19	chr9:97823600-97845000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:97824200-97832800	Strong transcription	Adipose Nuclei	Adipose
21	chr9:97824600-97832200	Strong transcription	Fetal Lung	lung
22	chr9:97824800-97832000	Enhancers	Fetal Heart	heart
23	chr9:97824800-97844600	Weak transcription	Fetal Thymus	thymus
24	chr9:97825200-97841000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:97825400-97830600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr9:97825800-97839200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:97825800-97843400	Weak transcription	Thymus	Thymus
29	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr9:97826000-97842800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:97826200-97843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:97826200-97847400	Weak transcription	HUVEC	blood vessel
33	chr9:97826400-97842800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:97826400-97844200	Weak transcription	GM12878-XiMat	blood
35	chr9:97826600-97835200	Weak transcription	Spleen	Spleen
36	chr9:97827000-97830800	Genic enhancers	NHLF	lung
37	chr9:97827000-97830800	Genic enhancers	Osteobl	bone
38	chr9:97827000-97839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:97827600-97832200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:97827600-97832400	Weak transcription	Colonic Mucosa	Colon
41	chr9:97827600-97835600	Enhancers	Right Atrium	heart
42	chr9:97827800-97833400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:97827800-97841400	Genic enhancers	Liver	Liver
44	chr9:97828000-97831400	Genic enhancers	A549	lung
45	chr9:97828200-97830200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:97828200-97830200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:97828200-97831200	Weak transcription	Gastric	stomach
48	chr9:97828200-97832800	Weak transcription	Small Intestine	intestine
49	chr9:97828200-97838800	Strong transcription	Fetal Intestine Large	intestine
50	chr9:97828400-97830400	Strong transcription	NHEK	skin

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