Variant report

Variant	rs2061801
Chromosome Location	chr9:97798381-97798382
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97793038..97795418-chr9:97797884..97800566,2	K562	blood:
2	chr9:97796997..97799888-chr9:97851480..97854262,2	MCF-7	breast:
3	chr9:97796632..97799193-chr9:97809608..97812323,2	MCF-7	breast:
4	chr9:97544575..97547315-chr9:97798052..97799769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap];0.90[AMR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1871220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356685	1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3739748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs475413	1.00[JPT][hapmap]
rs6479578	1.00[CEU][hapmap]
rs6479589	0.90[AMR][1000 genomes]
rs6479596	0.91[EUR][1000 genomes]
rs6479597	0.91[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7022963	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750359	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750367	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72750373	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[ASN][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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:97791600-97799600	Weak transcription	Hela-S3	cervix
4	chr9:97791600-97800000	Weak transcription	Placenta	Placenta
5	chr9:97793000-97800000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:97793200-97802200	Weak transcription	Fetal Kidney	kidney
7	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
8	chr9:97793800-97800000	Weak transcription	Adipose Nuclei	Adipose
9	chr9:97794000-97799800	Weak transcription	Fetal Lung	lung
10	chr9:97794200-97805800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:97794400-97806000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:97794600-97800000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:97794600-97800000	Weak transcription	Colonic Mucosa	Colon
15	chr9:97794600-97805000	Weak transcription	Fetal Thymus	thymus
16	chr9:97794800-97799800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:97795000-97799200	Weak transcription	HMEC	breast
18	chr9:97795000-97802200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:97795200-97804000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:97795400-97799000	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:97795400-97800000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr9:97795400-97800000	Weak transcription	Gastric	stomach
24	chr9:97795400-97803000	Enhancers	Colon Smooth Muscle	Colon
25	chr9:97795400-97806200	Genic enhancers	A549	lung
26	chr9:97795600-97798400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr9:97795600-97799000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr9:97795600-97799000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:97795600-97799200	Weak transcription	NH-A	brain
30	chr9:97795600-97799800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr9:97795600-97802200	Weak transcription	Spleen	Spleen
32	chr9:97795600-97806000	Weak transcription	Lung	lung
33	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:97795800-97798400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:97795800-97798400	Weak transcription	Brain Hippocampus Middle	brain
36	chr9:97795800-97798400	Weak transcription	Fetal Muscle Leg	muscle
37	chr9:97795800-97799000	Weak transcription	Brain Anterior Caudate	brain
38	chr9:97795800-97799000	Weak transcription	Esophagus	oesophagus
39	chr9:97795800-97799000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr9:97795800-97799000	Weak transcription	Stomach Mucosa	stomach
41	chr9:97795800-97799200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:97795800-97800000	Weak transcription	Right Atrium	heart
43	chr9:97795800-97802200	Weak transcription	Small Intestine	intestine
44	chr9:97796000-97798800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr9:97796000-97798800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:97796000-97799000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:97796000-97800800	Strong transcription	HepG2	liver
48	chr9:97796600-97799000	Weak transcription	Aorta	Aorta
49	chr9:97796600-97802200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr9:97797000-97798600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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