Variant report

Variant	rs2255797
Chromosome Location	chr12:104245866-104245867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104233313..104235106-chr12:104245857..104249514,3	MCF-7	breast:
2	chr12:104232946..104237794-chr12:104239535..104249085,16	K562	blood:
3	chr12:104244166..104246985-chr12:104247469..104250168,2	MCF-7	breast:
4	chr12:104242898..104244862-chr12:104245301..104247034,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10778305	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs1165593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1165668	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1165669	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs1165670	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs1165675	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1165679	0.83[TSI][hapmap]
rs12812668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12816861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12822228	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12822539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1370410	0.90[MEX][hapmap]
rs1370411	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370413	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370775	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1370776	0.90[MEX][hapmap]
rs1370780	0.90[MEX][hapmap]
rs17034734	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs1866071	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap]
rs1992207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992208	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118312	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2252325	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2252327	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255296	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255303	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255316	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2255584	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255794	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs2255795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs2255799	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][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]
rs2256160	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2256303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2438111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2438112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2438113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2438114	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438388	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2576954	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2576956	0.83[TSI][hapmap]
rs2576971	0.83[TSI][hapmap]
rs2578010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35015549	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4453308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4453309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4964302	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4964304	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71466281	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71466282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71466283	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7973043	0.93[ASN][1000 genomes]
rs7973278	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7973401	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9669708	0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2255797	ALDH1L2	cis	parietal	SCAN
rs2255797	VSTM2B	trans	cerebellum	SCAN
rs2255797	NT5DC3	cis	parietal	SCAN
rs2255797	GLT8D2	cis	parietal	SCAN
rs2255797	MIR3652	cis	Esophagus Mucosa	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104236000-104252600	Weak transcription	Esophagus	oesophagus
2	chr12:104236000-104252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:104236000-104253600	Weak transcription	Gastric	stomach
4	chr12:104236200-104246400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:104236400-104246000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:104236600-104248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:104238200-104246400	Weak transcription	Fetal Intestine Large	intestine
8	chr12:104240000-104247600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
10	chr12:104241800-104246400	Weak transcription	Fetal Intestine Small	intestine
11	chr12:104242200-104246400	Weak transcription	Fetal Lung	lung
12	chr12:104242200-104248400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:104242400-104246400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:104242600-104246800	Enhancers	HMEC	breast
15	chr12:104242800-104246200	Weak transcription	Pancreas	Pancrea
16	chr12:104242800-104247000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:104243000-104246000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:104243400-104246000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:104243600-104246400	Weak transcription	Aorta	Aorta
20	chr12:104243800-104251400	Enhancers	Colon Smooth Muscle	Colon
21	chr12:104244400-104246200	Enhancers	NH-A	brain
22	chr12:104244400-104246800	Enhancers	Brain Anterior Caudate	brain
23	chr12:104244400-104246800	Enhancers	Osteobl	bone
24	chr12:104244600-104246200	Enhancers	Brain Substantia Nigra	brain
25	chr12:104244600-104247000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:104244800-104246000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:104244800-104246600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:104244800-104246800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:104245000-104246800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:104245000-104246800	Enhancers	Brain Cingulate Gyrus	brain
31	chr12:104245000-104247000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr12:104245000-104250800	Enhancers	HepG2	liver
33	chr12:104245200-104246000	Weak transcription	NHEK	skin
34	chr12:104245200-104247000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:104245200-104247000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr12:104245200-104252000	Enhancers	Stomach Smooth Muscle	stomach
37	chr12:104245600-104246400	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr12:104245600-104246800	Enhancers	Fetal Stomach	stomach
39	chr12:104245600-104246800	Enhancers	HSMM	muscle
40	chr12:104245600-104249400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:104245800-104246200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:104245800-104246600	Enhancers	Brain Angular Gyrus	brain
43	chr12:104245800-104248200	Weak transcription	Liver	Liver

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