Variant report

Variant	rs2408498
Chromosome Location	chr12:46796900-46796901
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	chr12:46781039..46783581-chr12:46796813..46799166,3	K562	blood:
7	chr12:46759584..46762474-chr12:46794055..46796996,3	K562	blood:
8	chr12:46796512..46798026-chr12:46803441..46805172,2	MCF-7	breast:
9	chr12:46778629..46780721-chr12:46796448..46799296,3	K562	blood:
10	chr12:46795569..46797516-chr12:46843995..46846223,2	K562	blood:

No data

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

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10748448	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748450	0.87[EUR][1000 genomes]
rs10785627	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785628	0.86[EUR][1000 genomes]
rs10785629	0.87[EUR][1000 genomes]
rs10880966	0.92[AMR][1000 genomes]
rs10880967	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880969	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880970	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880971	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10880973	0.87[EUR][1000 genomes]
rs11183478	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183479	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183483	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183484	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11183486	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11183488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1125909	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11561535	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12099669	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12298616	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12314541	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319162	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12813763	0.86[AMR][1000 genomes]
rs12814298	0.80[AMR][1000 genomes]
rs12814341	0.86[AMR][1000 genomes]
rs12822345	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12824565	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12832425	0.86[AMR][1000 genomes]
rs12832777	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1472178	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1472179	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1492895	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131371	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2220727	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408497	0.94[AMR][1000 genomes]
rs2897951	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936214	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4072304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4076247	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4077707	0.84[EUR][1000 genomes]
rs4077708	0.86[EUR][1000 genomes]
rs4258438	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4427617	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768118	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768119	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768121	0.83[AMR][1000 genomes]
rs4768122	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768123	0.85[EUR][1000 genomes]
rs4768699	0.85[ASN][1000 genomes]
rs4768709	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768710	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768711	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768712	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768713	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768714	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768715	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768716	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768717	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768718	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768719	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768723	0.86[EUR][1000 genomes]
rs4768724	0.87[EUR][1000 genomes]
rs4768725	0.87[EUR][1000 genomes]
rs6582641	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6582642	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6582643	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6582645	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582646	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6582657	0.87[EUR][1000 genomes]
rs6582658	0.87[EUR][1000 genomes]
rs7134289	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7134505	0.83[ASN][1000 genomes]
rs7301001	0.83[AMR][1000 genomes]
rs7311504	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7312259	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7485580	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485599	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7486495	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7486532	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7486580	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7487828	0.83[AMR][1000 genomes]
rs7487877	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488450	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7489242	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7953450	0.85[ASN][1000 genomes]
rs7959731	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7968897	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7976280	0.94[AMR][1000 genomes]
rs9669404	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9971879	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:91 , 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	chr12:46787000-46798400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:46787800-46798200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:46789800-46797600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:46793800-46801200	Enhancers	Dnd41	blood
7	chr12:46794200-46798600	Enhancers	Thymus	Thymus
8	chr12:46794200-46798800	Enhancers	Fetal Thymus	thymus
9	chr12:46794200-46799000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:46794200-46799000	Enhancers	Osteobl	bone
11	chr12:46794200-46799600	Enhancers	Primary T cells from cord blood	blood
12	chr12:46794400-46797600	Enhancers	NHEK	skin
13	chr12:46794400-46797800	Enhancers	HepG2	liver
14	chr12:46794400-46798400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:46794400-46798800	Enhancers	Colon Smooth Muscle	Colon
16	chr12:46794400-46798800	Enhancers	NHDF-Ad	bronchial
17	chr12:46794400-46799000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:46794400-46799000	Enhancers	HSMMtube	muscle
19	chr12:46794400-46799000	Enhancers	NHLF	lung
20	chr12:46794600-46798600	Enhancers	Fetal Stomach	stomach
21	chr12:46794600-46798800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:46794600-46798800	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:46794800-46798800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:46794800-46802200	Weak transcription	Placenta	Placenta
25	chr12:46795000-46798200	Enhancers	Fetal Heart	heart
26	chr12:46795000-46809200	Weak transcription	Esophagus	oesophagus
27	chr12:46795200-46797400	Enhancers	Stomach Smooth Muscle	stomach
28	chr12:46795200-46798400	Enhancers	Fetal Lung	lung
29	chr12:46795200-46798400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr12:46795400-46797000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr12:46795400-46797600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:46795400-46797800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr12:46795400-46797800	Enhancers	Stomach Mucosa	stomach
34	chr12:46795400-46798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:46795400-46798200	Weak transcription	Left Ventricle	heart
36	chr12:46795400-46798400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:46795400-46798400	Weak transcription	Spleen	Spleen
38	chr12:46795400-46798600	Enhancers	HSMM	muscle
39	chr12:46795600-46797000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:46795600-46797000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:46795600-46797400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:46795600-46797400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr12:46795600-46798200	Weak transcription	Psoas Muscle	Psoas
44	chr12:46795600-46798400	Weak transcription	Right Atrium	heart
45	chr12:46795600-46798600	Enhancers	HMEC	breast
46	chr12:46795800-46797000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr12:46795800-46797800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:46795800-46797800	Enhancers	A549	lung
49	chr12:46795800-46798200	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:46795800-46798600	Enhancers	HUVEC	blood vessel

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