Variant report

Variant	rs4760684
Chromosome Location	chr12:48518080-48518081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48515800..48518794-chr12:48562400..48565355,2	K562	blood:
2	chr12:48503405..48506326-chr12:48517186..48520007,2	K562	blood:
3	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000257885	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10082861	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10219623	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10219645	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875745	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875746	0.95[ASN][1000 genomes]
rs10875747	0.97[ASN][1000 genomes]
rs10875748	0.97[ASN][1000 genomes]
rs10875750	0.95[ASN][1000 genomes]
rs10875756	0.87[ASN][1000 genomes]
rs11168413	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168414	0.97[ASN][1000 genomes]
rs11168415	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168416	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168418	0.97[ASN][1000 genomes]
rs11168420	0.90[ASN][1000 genomes]
rs11168421	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168422	0.97[ASN][1000 genomes]
rs11168425	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168427	0.94[ASN][1000 genomes]
rs11168433	0.87[ASN][1000 genomes]
rs12297470	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12306290	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12310813	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12312134	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17122666	0.91[ASN][1000 genomes]
rs1859445	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107638	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228500	0.97[ASN][1000 genomes]
rs2269933	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269935	0.97[ASN][1000 genomes]
rs2286021	0.95[ASN][1000 genomes]
rs4760619	0.90[ASN][1000 genomes]
rs4760681	0.95[ASN][1000 genomes]
rs4760687	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760689	0.87[ASN][1000 genomes]
rs4760690	0.87[ASN][1000 genomes]
rs60106007	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61343568	0.94[ASN][1000 genomes]
rs725454	0.91[ASN][1000 genomes]
rs7485355	0.95[ASN][1000 genomes]
rs7486424	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8804	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4760684	RP1-228P16.1	cis	Thyroid	GTEx
rs4760684	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760684	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48513400-48524800	Weak transcription	Liver	Liver
2	chr12:48513400-48526600	Weak transcription	Spleen	Spleen
3	chr12:48513600-48526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:48513600-48527000	Weak transcription	Pancreas	Pancrea
5	chr12:48513800-48519400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:48513800-48524400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:48513800-48525000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:48513800-48525000	Weak transcription	Lung	lung
9	chr12:48513800-48525800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:48513800-48526000	Weak transcription	Colonic Mucosa	Colon
11	chr12:48513800-48526400	Weak transcription	Gastric	stomach
12	chr12:48513800-48526600	Weak transcription	Thymus	Thymus
13	chr12:48513800-48526800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:48514000-48518600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:48514000-48520200	Weak transcription	Fetal Lung	lung
16	chr12:48514000-48520600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:48514000-48521200	Weak transcription	Primary B cells from cord blood	blood
18	chr12:48514000-48522000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:48514000-48522200	Weak transcription	Adipose Nuclei	Adipose
20	chr12:48514000-48523200	Weak transcription	Fetal Kidney	kidney
21	chr12:48514000-48524200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr12:48514000-48524200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:48514000-48524600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:48514000-48525000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:48514000-48525000	Weak transcription	Brain Substantia Nigra	brain
26	chr12:48514000-48525000	Weak transcription	Esophagus	oesophagus
27	chr12:48514000-48525600	Weak transcription	Placenta	Placenta
28	chr12:48514000-48526400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:48514000-48526600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:48514000-48526600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:48514000-48536600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:48514000-48537200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:48514200-48518200	Weak transcription	A549	lung
34	chr12:48514200-48523200	Weak transcription	HSMMtube	muscle
35	chr12:48514200-48527000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:48514400-48518200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:48514400-48518400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:48514400-48519400	Weak transcription	Aorta	Aorta
39	chr12:48514400-48523200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:48514400-48525400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:48514400-48526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:48514600-48519800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:48514600-48520000	Weak transcription	NHEK	skin
44	chr12:48514600-48526200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr12:48514800-48526000	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:48515200-48518200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:48515200-48523400	Weak transcription	Dnd41	blood
48	chr12:48515400-48522200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr12:48515600-48535600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:48515800-48519000	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links