Variant report

Variant	rs4907312
Chromosome Location	chr2:97033940-97033941
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97024759..97027448-chr2:97032041..97034944,2	MCF-7	breast:
2	chr2:97027281..97029651-chr2:97031268..97034024,2	K562	blood:
3	chr2:97032551..97034623-chr2:97038174..97040150,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1044594	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs1048675	0.92[CEU][hapmap]
rs11903461	0.92[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs12614188	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17420101	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs17479466	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap]
rs17633463	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2085842	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2276649	0.92[CEU][hapmap]
rs2279105	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs2305935	0.91[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3171927	0.90[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap]
rs3214058	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs3214063	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs3731930	0.84[CEU][hapmap]
rs3731935	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap]
rs4907231	0.82[AMR][1000 genomes]
rs4907233	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4907307	0.84[CEU][hapmap]
rs4907310	0.92[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs4907311	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs56027554	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56221936	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58328293	0.81[AMR][1000 genomes]
rs62153041	0.81[AMR][1000 genomes]
rs62153898	0.82[AMR][1000 genomes]
rs62153900	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62153901	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153902	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62153905	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62153906	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62153915	0.84[AMR][1000 genomes]
rs62153917	0.92[ASN][1000 genomes]
rs62153922	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62153923	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62154786	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62154787	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6737429	0.92[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6755877	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][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	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
8	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4907312	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4907312	AC008268.2	cis	lung	GTEx
rs4907312	AC008268.2	cis	Thyroid	GTEx
rs4907312	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs4907312	CIAO1	cis	Esophagus Mucosa	GTEx
rs4907312	CIAO1	cis	Adipose Subcutaneous	GTEx
rs4907312	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs4907312	CIAO1	cis	lymphoblastoid	seeQTL
rs4907312	AC008268.2	cis	Artery Tibial	GTEx
rs4907312	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97002000-97036000	Weak transcription	Gastric	stomach
2	chr2:97002200-97037600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:97002800-97040000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:97004000-97040400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:97004200-97040400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:97006200-97041000	Strong transcription	Dnd41	blood
7	chr2:97006600-97040200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:97006600-97040400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:97006800-97040400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:97006800-97040600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:97006800-97040800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:97007000-97040600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:97007200-97040000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:97007200-97040200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:97007200-97040400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr2:97007200-97041600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:97007400-97040200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:97007400-97040400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:97007400-97040600	Strong transcription	Thymus	Thymus
20	chr2:97011200-97038000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:97011400-97038400	Strong transcription	GM12878-XiMat	blood
22	chr2:97012400-97037600	Weak transcription	Colonic Mucosa	Colon
23	chr2:97012600-97035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:97012600-97040000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:97013800-97040000	Weak transcription	Esophagus	oesophagus
26	chr2:97014800-97040600	Strong transcription	A549	lung
27	chr2:97015000-97039600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:97016800-97035800	Weak transcription	Brain Germinal Matrix	brain
29	chr2:97017000-97040000	Weak transcription	Fetal Kidney	kidney
30	chr2:97019200-97035000	Weak transcription	Placenta	Placenta
31	chr2:97019200-97040600	Strong transcription	Fetal Thymus	thymus
32	chr2:97019200-97042000	Weak transcription	Spleen	Spleen
33	chr2:97020000-97039200	Weak transcription	Fetal Heart	heart
34	chr2:97020000-97041400	Weak transcription	HSMM	muscle
35	chr2:97020200-97035600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:97020200-97037000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:97024400-97040000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:97024600-97040000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr2:97024800-97036800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:97024800-97039800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:97024800-97039800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:97024800-97040000	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:97025000-97037400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:97025600-97034600	Weak transcription	Brain Anterior Caudate	brain
45	chr2:97025600-97034600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:97025600-97039600	Weak transcription	Pancreas	Pancrea
47	chr2:97026400-97038000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:97026400-97038200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:97026600-97037800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:97026800-97037800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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