Variant report

Variant	rs3802449
Chromosome Location	chr9:97846255-97846256
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:97846029-97846353	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr9:97836122-97846291	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97840496..97842438-chr9:97844995..97846708,2	MCF-7	breast:
2	chr9:97844149..97846722-chr9:97853802..97855942,2	K562	blood:
3	chr9:97845277..97847054-chr9:97867436..97869989,2	K562	blood:

Variant related genes	Relation type
MIR27B	TF binding region
MIR23B	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12683030	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12683182	0.85[JPT][hapmap]
rs12683564	0.86[ASN][1000 genomes]
rs12683692	0.91[ASN][1000 genomes]
rs12686588	0.85[JPT][hapmap]
rs2061799	0.86[JPT][hapmap]
rs2404458	0.85[JPT][hapmap]
rs3780566	0.85[JPT][hapmap]
rs3802450	0.86[ASN][1000 genomes]
rs4647402	0.85[JPT][hapmap]
rs4647408	0.85[JPT][hapmap]
rs4647414	0.85[JPT][hapmap]
rs4647436	0.86[JPT][hapmap]
rs4647437	0.86[JPT][hapmap]
rs4647466	0.85[JPT][hapmap]
rs4647472	0.86[JPT][hapmap]
rs4647473	0.85[JPT][hapmap]
rs4647484	0.85[JPT][hapmap]
rs4647491	0.86[JPT][hapmap]
rs4647493	0.85[JPT][hapmap]
rs4647509	0.85[JPT][hapmap]
rs4647514	0.85[JPT][hapmap]
rs4647516	0.85[JPT][hapmap]
rs4647549	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6479596	0.88[JPT][hapmap]
rs6479597	0.88[JPT][hapmap]
rs7022739	0.86[JPT][hapmap]
rs72750391	0.86[ASN][1000 genomes]
rs7854840	0.86[JPT][hapmap]
rs9792415	0.85[JPT][hapmap]
rs9792533	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
6	esv3341854	chr9:97843531-97848029	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	266 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97813000-97873000	Weak transcription	K562	blood
2	chr9:97820000-97854200	Weak transcription	Fetal Brain Male	brain
3	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97825400-97854400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr9:97825800-97852600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr9:97826200-97847400	Weak transcription	HUVEC	blood vessel
7	chr9:97838000-97871200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr9:97839600-97850400	Strong transcription	HepG2	liver
9	chr9:97839600-97851000	Genic enhancers	A549	lung
10	chr9:97840000-97850000	Strong transcription	Osteobl	bone
11	chr9:97840800-97851800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr9:97841200-97849800	Strong transcription	NH-A	brain
13	chr9:97841200-97864400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:97841400-97853000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:97841600-97847000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:97841600-97849200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr9:97841600-97850000	Strong transcription	NHLF	lung
18	chr9:97841600-97855000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:97841800-97851600	Strong transcription	Fetal Intestine Small	intestine
20	chr9:97841800-97853800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:97841800-97854000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr9:97842200-97847200	Weak transcription	Dnd41	blood
23	chr9:97842200-97847600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:97842200-97848200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:97842200-97849600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:97842200-97850600	Strong transcription	Fetal Lung	lung
27	chr9:97842200-97852000	Strong transcription	NHEK	skin
28	chr9:97842400-97850000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:97842400-97850200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:97842400-97852600	Strong transcription	Fetal Intestine Large	intestine
31	chr9:97842400-97854200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:97842800-97846800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:97842800-97849400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:97842800-97849400	Strong transcription	NHDF-Ad	bronchial
35	chr9:97842800-97849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:97842800-97850800	Strong transcription	Placenta	Placenta
37	chr9:97843000-97846800	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr9:97843000-97848400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr9:97843000-97849200	Strong transcription	Primary T cells from cord blood	blood
40	chr9:97843000-97850200	Strong transcription	Adipose Nuclei	Adipose
41	chr9:97843200-97846400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:97843200-97846400	Genic enhancers	Brain Angular Gyrus	brain
43	chr9:97843200-97847800	Strong transcription	Aorta	Aorta
44	chr9:97843200-97849000	Genic enhancers	Brain Cingulate Gyrus	brain
45	chr9:97843200-97849200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:97843200-97849400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:97843200-97851600	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr9:97843200-97851800	Genic enhancers	Brain Hippocampus Middle	brain
49	chr9:97843200-97852400	Genic enhancers	Rectal Smooth Muscle	rectum
50	chr9:97843400-97849800	Strong transcription	Hela-S3	cervix

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