Variant report

Variant	rs2408497
Chromosome Location	chr12:46796751-46796752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46795533..46798124-chr12:46799552..46803946,3	K562	blood:
2	chr12:46794174..46798124-chr12:46799495..46805327,7	K562	blood:
3	chr12:46776484..46782223-chr12:46794471..46799373,6	MCF-7	breast:
4	chr12:46787652..46790315-chr12:46793888..46796934,3	K562	blood:
5	chr12:46793862..46797366-chr12:46798440..46803120,6	MCF-7	breast:
6	chr12:46759584..46762474-chr12:46794055..46796996,3	K562	blood:
7	chr12:46796512..46798026-chr12:46803441..46805172,2	MCF-7	breast:
8	chr12:46778629..46780721-chr12:46796448..46799296,3	K562	blood:
9	chr12:46795569..46797516-chr12:46843995..46846223,2	K562	blood:
10	chr12:46795170..46796773-chr12:46824331..46826710,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000257496	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10467213	0.83[AMR][1000 genomes]
rs10748448	0.92[AMR][1000 genomes]
rs10785627	0.88[AMR][1000 genomes]
rs1079780	0.83[AMR][1000 genomes]
rs10880961	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10880962	0.82[CEU][hapmap]
rs10880966	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880967	0.90[AMR][1000 genomes]
rs10880968	0.88[AMR][1000 genomes]
rs10880969	0.85[AMR][1000 genomes]
rs10880970	0.84[AMR][1000 genomes]
rs11183468	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11183478	0.85[AMR][1000 genomes]
rs11183479	0.85[AMR][1000 genomes]
rs11183483	0.85[AMR][1000 genomes]
rs11183484	0.82[AMR][1000 genomes]
rs11183486	0.80[AMR][1000 genomes]
rs1125909	0.88[AMR][1000 genomes]
rs11534993	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12099669	0.88[AMR][1000 genomes]
rs12314541	0.92[AMR][1000 genomes]
rs12319162	0.82[AMR][1000 genomes]
rs12320197	0.81[CEU][hapmap]
rs12813763	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814298	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12814341	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12816358	0.83[AMR][1000 genomes]
rs12822345	0.81[AMR][1000 genomes]
rs12824565	0.81[AMR][1000 genomes]
rs12832425	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12832777	0.81[AMR][1000 genomes]
rs1472178	0.88[AMR][1000 genomes]
rs1472179	0.88[AMR][1000 genomes]
rs1492895	0.91[AMR][1000 genomes]
rs1873793	0.81[CEU][hapmap]
rs2131371	0.90[AMR][1000 genomes]
rs2169030	0.83[CHB][hapmap]
rs2220727	0.89[AMR][1000 genomes]
rs2279559	0.81[CEU][hapmap]
rs2408498	0.94[AMR][1000 genomes]
rs2408504	0.83[AMR][1000 genomes]
rs2408507	0.81[AMR][1000 genomes]
rs2897951	0.91[AMR][1000 genomes]
rs2897968	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3936214	0.80[AMR][1000 genomes]
rs4072304	0.85[AMR][1000 genomes]
rs4076247	0.84[AMR][1000 genomes]
rs4076248	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs4076484	0.82[EUR][1000 genomes]
rs4258438	0.89[AMR][1000 genomes]
rs4427617	0.90[AMR][1000 genomes]
rs4586238	0.83[AMR][1000 genomes]
rs4768118	0.90[AMR][1000 genomes]
rs4768119	0.89[AMR][1000 genomes]
rs4768121	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4768122	0.81[AMR][1000 genomes]
rs4768696	0.83[AMR][1000 genomes]
rs4768709	0.89[AMR][1000 genomes]
rs4768710	0.91[AMR][1000 genomes]
rs4768711	0.85[AMR][1000 genomes]
rs4768712	0.90[AMR][1000 genomes]
rs4768713	0.90[AMR][1000 genomes]
rs4768714	0.90[AMR][1000 genomes]
rs4768715	0.82[AMR][1000 genomes]
rs4768716	0.81[AMR][1000 genomes]
rs4768717	0.84[AMR][1000 genomes]
rs4768718	0.84[AMR][1000 genomes]
rs6582641	0.89[AMR][1000 genomes]
rs6582642	0.84[AMR][1000 genomes]
rs6582643	0.84[AMR][1000 genomes]
rs6582645	0.89[AMR][1000 genomes]
rs6582646	0.85[AMR][1000 genomes]
rs6582656	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7134289	0.82[AMR][1000 genomes]
rs7301001	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7311504	0.84[AMR][1000 genomes]
rs7312259	0.90[AMR][1000 genomes]
rs7485580	0.84[AMR][1000 genomes]
rs7485599	0.81[AMR][1000 genomes]
rs7486495	0.88[AMR][1000 genomes]
rs7486580	0.88[AMR][1000 genomes]
rs7487075	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7487877	0.86[AMR][1000 genomes]
rs7488450	0.85[AMR][1000 genomes]
rs7489242	0.85[AMR][1000 genomes]
rs7958774	0.83[AMR][1000 genomes]
rs7959731	0.82[AMR][1000 genomes]
rs7961994	0.80[CEU][hapmap]
rs7968897	0.88[AMR][1000 genomes]
rs7976280	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979418	0.84[CEU][hapmap];0.80[AMR][1000 genomes]
rs9669404	0.94[AMR][1000 genomes]
rs9971879	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46778800-46797200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
3	chr12:46783200-46796800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:46787000-46798400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:46787800-46798200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:46789600-46796800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:46789800-46797600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:46791000-46796800	Weak transcription	Ovary	ovary
9	chr12:46793800-46796800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:46793800-46801200	Enhancers	Dnd41	blood
11	chr12:46794200-46796800	Enhancers	NH-A	brain
12	chr12:46794200-46798600	Enhancers	Thymus	Thymus
13	chr12:46794200-46798800	Enhancers	Fetal Thymus	thymus
14	chr12:46794200-46799000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:46794200-46799000	Enhancers	Osteobl	bone
16	chr12:46794200-46799600	Enhancers	Primary T cells from cord blood	blood
17	chr12:46794400-46796800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:46794400-46797600	Enhancers	NHEK	skin
19	chr12:46794400-46797800	Enhancers	HepG2	liver
20	chr12:46794400-46798400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr12:46794400-46798800	Enhancers	Colon Smooth Muscle	Colon
22	chr12:46794400-46798800	Enhancers	NHDF-Ad	bronchial
23	chr12:46794400-46799000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:46794400-46799000	Enhancers	HSMMtube	muscle
25	chr12:46794400-46799000	Enhancers	NHLF	lung
26	chr12:46794600-46798600	Enhancers	Fetal Stomach	stomach
27	chr12:46794600-46798800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:46794600-46798800	Enhancers	Rectal Smooth Muscle	rectum
29	chr12:46794800-46798800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr12:46794800-46802200	Weak transcription	Placenta	Placenta
31	chr12:46795000-46798200	Enhancers	Fetal Heart	heart
32	chr12:46795000-46809200	Weak transcription	Esophagus	oesophagus
33	chr12:46795200-46797400	Enhancers	Stomach Smooth Muscle	stomach
34	chr12:46795200-46798400	Enhancers	Fetal Lung	lung
35	chr12:46795200-46798400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr12:46795400-46797000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr12:46795400-46797600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:46795400-46797800	Enhancers	H1 Cell Line	embryonic stem cell
39	chr12:46795400-46797800	Enhancers	Stomach Mucosa	stomach
40	chr12:46795400-46798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:46795400-46798200	Weak transcription	Left Ventricle	heart
42	chr12:46795400-46798400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr12:46795400-46798400	Weak transcription	Spleen	Spleen
44	chr12:46795400-46798600	Enhancers	HSMM	muscle
45	chr12:46795600-46796800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:46795600-46797000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:46795600-46797000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:46795600-46797400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr12:46795600-46797400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr12:46795600-46798200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links