Variant report

Variant	rs9289985
Chromosome Location	chr3:99878116-99878117
allele	C/G
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	EP300	chr3:99878075-99878768	SK-N-SH_RA	brain:	n/a	chr3:99878563-99878572
2	EP300	chr3:99876484-99879473	SK-N-SH	brain:	n/a	chr3:99878563-99878572
3	EP300	chr3:99878074-99878799	SK-N-SH	brain:	n/a	chr3:99878563-99878572
4	GATA2	chr3:99877319-99879048	SH-SY5Y	brain:	n/a	chr3:99878805-99878815 chr3:99878342-99878358 chr3:99878677-99878691 chr3:99877795-99877808
5	TCF12	chr3:99877426-99879157	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr3:99877537-99879139	SK-N-SH	brain:	n/a	n/a
7	JUND	chr3:99877600-99878997	SK-N-SH	brain:	n/a	chr3:99878885-99878895 chr3:99878224-99878236
8	JUND	chr3:99877671-99878863	SK-N-SH	brain:	n/a	chr3:99878224-99878236
9	PBX3	chr3:99877638-99878917	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr3:99877652-99878946	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr3:99877430-99879224	SK-N-SH	brain:	n/a	chr3:99878805-99878815 chr3:99878342-99878358 chr3:99877795-99877808
12	GATA3	chr3:99877458-99879224	SH-SY5Y	brain:	n/a	chr3:99878805-99878815 chr3:99878342-99878358 chr3:99877795-99877808
13	CEBPB	chr3:99877961-99878149	A549	lung:	n/a	chr3:99878044-99878055
14	GATA3	chr3:99877393-99879250	SK-N-SH	brain:	n/a	chr3:99878805-99878815 chr3:99878342-99878358 chr3:99877795-99877808
15	CEBPB	chr3:99877863-99879053	IMR90	lung:	n/a	chr3:99878044-99878055
16	MEF2A	chr3:99878114-99878984	SK-N-SH	brain:	n/a	chr3:99878138-99878152 chr3:99878597-99878612 chr3:99878593-99878614 chr3:99878598-99878612 chr3:99878597-99878613
17	EP300	chr3:99877598-99878130	SK-N-SH_RA	brain:	n/a	n/a
18	TCF12	chr3:99877589-99879163	SK-N-SH	brain:	n/a	n/a
19	FOS	chr3:99878005-99878614	MCF10A-Er-Src	breast:	n/a	chr3:99878224-99878236
20	EP300	chr3:99877645-99878838	SK-N-SH	brain:	n/a	chr3:99878563-99878572
21	TEAD4	chr3:99877588-99878877	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr3:99877613-99878874	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr3:99877932-99878177	HepG2	liver:	n/a	chr3:99878044-99878055

Variant related genes	Relation type
CMSS1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10049383	0.80[CEU][hapmap]
rs10212525	0.81[CEU][hapmap]
rs11537816	1.00[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214372	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs1214373	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs13064704	0.81[CEU][hapmap]
rs13069311	0.81[CEU][hapmap];0.82[MKK][hapmap]
rs13093776	0.81[AMR][1000 genomes]
rs13323143	0.81[CEU][hapmap];0.82[MKK][hapmap]
rs1489816	0.81[CEU][hapmap]
rs17392948	0.86[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap]
rs277636	0.85[JPT][hapmap]
rs277652	0.85[JPT][hapmap]
rs277654	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs28394036	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28870092	0.83[AMR][1000 genomes]
rs4075038	0.81[CEU][hapmap]
rs4361315	0.81[CEU][hapmap]
rs4571265	0.81[CEU][hapmap]
rs4928149	0.86[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap]
rs62285478	0.82[AMR][1000 genomes]
rs6790877	0.91[CEU][hapmap]
rs6802422	0.81[CEU][hapmap]
rs7610486	0.81[CEU][hapmap];0.88[MKK][hapmap]
rs7618677	0.85[JPT][hapmap]
rs7620228	0.81[CEU][hapmap];0.82[MKK][hapmap]
rs7627991	0.81[CEU][hapmap];0.82[MKK][hapmap]
rs7637157	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs923470	0.81[CEU][hapmap]
rs923471	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs9816538	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823908	0.81[CEU][hapmap];0.88[MKK][hapmap]
rs9825882	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828079	0.81[CEU][hapmap];0.82[MKK][hapmap]
rs9833888	0.81[CEU][hapmap]
rs9833980	0.81[CEU][hapmap]
rs9837602	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs9839910	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841186	0.82[MKK][hapmap]
rs9851645	0.81[CEU][hapmap]
rs9853522	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854260	1.00[ASW][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9860290	0.82[ASW][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.91[AMR][1000 genomes]
rs9863738	1.00[CHD][hapmap];0.85[JPT][hapmap]
rs9864437	0.81[CEU][hapmap]
rs9873878	0.81[CEU][hapmap]
rs9875878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][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]
rs9880795	0.85[JPT][hapmap]
rs9882337	1.00[JPT][hapmap]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99864400-99886600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:99865600-99898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:99868000-99897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:99869000-99895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:99869000-99897800	Weak transcription	Pancreas	Pancrea
7	chr3:99870400-99898600	Weak transcription	Esophagus	oesophagus
8	chr3:99871400-99899400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:99874400-99894400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:99874400-99897000	Weak transcription	K562	blood
11	chr3:99874600-99878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:99874600-99879000	Weak transcription	Small Intestine	intestine
13	chr3:99874600-99885200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:99874600-99897400	Weak transcription	A549	lung
15	chr3:99874800-99878800	Weak transcription	Primary T cells from cord blood	blood
16	chr3:99874800-99886600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:99874800-99886600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:99874800-99891000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:99874800-99895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:99874800-99897200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:99874800-99897200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:99874800-99897200	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:99874800-99898200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:99874800-99898400	Weak transcription	HepG2	liver
25	chr3:99875000-99897400	Weak transcription	GM12878-XiMat	blood
26	chr3:99875200-99881000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:99875200-99886400	Weak transcription	Dnd41	blood
28	chr3:99875200-99886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:99875200-99887000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:99875400-99890400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:99875600-99878800	Weak transcription	Fetal Stomach	stomach
32	chr3:99876200-99878200	Enhancers	HUVEC	blood vessel
33	chr3:99876200-99878800	Enhancers	Fetal Heart	heart
34	chr3:99876400-99880400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:99876400-99885000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:99876400-99890400	Weak transcription	Primary B cells from cord blood	blood
37	chr3:99876400-99890800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:99876600-99879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:99876600-99880200	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:99876600-99880800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:99876600-99889200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:99876600-99894800	Weak transcription	Right Atrium	heart
43	chr3:99876600-99897200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:99876600-99897400	Weak transcription	Fetal Intestine Small	intestine
45	chr3:99876800-99878600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:99876800-99879000	Weak transcription	Left Ventricle	heart
47	chr3:99876800-99879200	Enhancers	Adipose Nuclei	Adipose
48	chr3:99876800-99879800	Enhancers	HSMMtube	muscle
49	chr3:99876800-99882400	Weak transcription	Aorta	Aorta
50	chr3:99876800-99886400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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