Variant report

Variant	rs2279105
Chromosome Location	chr2:96993757-96993758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:96969714..96973384-chr2:96993289..96996221,3	MCF-7	breast:
2	chr2:96988883..96991415-chr2:96992469..96994531,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144028	Chromatin interaction
ENSG00000198885	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1044594	0.83[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1048675	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11903461	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17420101	0.83[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17479466	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17633463	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2085842	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2276648	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276649	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2305935	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3171927	0.83[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs3214058	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3214063	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3731930	0.92[CEU][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3731935	0.80[CEU][hapmap];0.90[GIH][hapmap];0.82[TSI][hapmap]
rs4907231	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4907232	0.83[ASN][1000 genomes]
rs4907233	0.83[EUR][1000 genomes]
rs4907307	0.92[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4907308	0.85[AMR][1000 genomes]
rs4907309	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4907310	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4907311	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4907312	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap]
rs56221936	0.82[EUR][1000 genomes]
rs56800261	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57406815	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58328293	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59966106	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59979953	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62153033	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62153034	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62153035	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153039	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62153041	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62153898	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62153900	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62153901	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62153902	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62153905	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62153906	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62153915	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6737429	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs7562544	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	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
9	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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2279105	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs2279105	AC008268.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2279105	AC008268.2	cis	Artery Tibial	GTEx
rs2279105	AC008268.2	cis	Muscle Skeletal	GTEx
rs2279105	CIAO1	cis	Whole Blood	GTEx
rs2279105	AC008268.2	cis	lung	GTEx
rs2279105	MGAT4A	cis	parietal	SCAN
rs2279105	CIAO1	cis	Skin Sun Exposed Lower leg	GTEx
rs2279105	CIAO1	cis	lung	GTEx
rs2279105	CIAO1	Cis_1M	lymphoblastoid	RTeQTL
rs2279105	AC008268.2	cis	Artery Aorta	GTEx
rs2279105	CIAO1	cis	lymphoblastoid	seeQTL
rs2279105	CIAO1	cis	Adipose Subcutaneous	GTEx
rs2279105	CIAO1	cis	Lymphoblastoid	GTEx
rs2279105	AC008268.2	cis	Nerve Tibial	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96991600-96996000	Weak transcription	Liver	Liver
2	chr2:96991600-97000400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:96991600-97000400	Weak transcription	Lung	lung
4	chr2:96991800-96995000	Weak transcription	NH-A	brain
5	chr2:96991800-96995000	Weak transcription	Osteobl	bone
6	chr2:96991800-97000400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:96991800-97000400	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:96991800-97000400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:96991800-97000400	Weak transcription	Fetal Kidney	kidney
10	chr2:96991800-97000400	Weak transcription	Right Atrium	heart
11	chr2:96991800-97000800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:96991800-97000800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:96992000-96995000	Weak transcription	NHDF-Ad	bronchial
14	chr2:96992000-96995400	Weak transcription	NHLF	lung
15	chr2:96992000-96995600	Weak transcription	Left Ventricle	heart
16	chr2:96992200-96994600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:96992200-96994800	Strong transcription	Fetal Stomach	stomach
18	chr2:96992200-96995000	Weak transcription	HUVEC	blood vessel
19	chr2:96992200-96995600	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:96992200-97000400	Weak transcription	Primary B cells from cord blood	blood
21	chr2:96992200-97000400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:96992200-97000400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:96992200-97000400	Weak transcription	Pancreas	Pancrea
24	chr2:96992200-97000600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:96992400-96993800	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr2:96992400-96993800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:96992400-96994000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:96992400-96994600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:96992400-96994800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:96992400-96994800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:96992400-96994800	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:96992400-96999600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:96992400-97000400	Weak transcription	Primary T cells from cord blood	blood
34	chr2:96992400-97000600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:96992400-97000600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:96992600-96993800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr2:96992600-96994200	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr2:96992600-96994200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:96992600-96994400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:96992600-96994400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:96992600-96994600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:96992600-96994600	Strong transcription	HepG2	liver
43	chr2:96992600-96994800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:96992600-96995400	Genic enhancers	Dnd41	blood
45	chr2:96992600-96996000	Strong transcription	Thymus	Thymus
46	chr2:96992600-96997800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:96992600-96999600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:96992600-97000400	Weak transcription	Esophagus	oesophagus
49	chr2:96992600-97000400	Weak transcription	Fetal Intestine Small	intestine
50	chr2:96992600-97000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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