Variant report

Variant	rs12468086
Chromosome Location	chr2:99320574-99320575
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	chr2:99320303..99322866-chr2:99324363..99327818,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10165386	0.92[CEU][hapmap]
rs10172913	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10199926	0.87[CEU][hapmap]
rs1028144	0.86[ASW][hapmap]
rs10496329	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12464653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467276	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469616	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17514013	0.81[MEX][hapmap];0.81[MKK][hapmap]
rs17755756	0.86[MEX][hapmap]
rs2309434	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2871235	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];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754870	0.86[ASW][hapmap]
rs3769688	0.81[MKK][hapmap]
rs3769689	0.87[ASW][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap]
rs55633363	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55646762	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56027617	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56354279	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56363239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56375699	0.87[ASN][1000 genomes]
rs60889948	0.84[ASN][1000 genomes]
rs62158010	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62158015	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62158019	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62158020	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62158022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6711574	0.87[MEX][hapmap]
rs6742760	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882164	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv2841	chr2:99296874-99342362	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99293400-99325200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr2:99295000-99325200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:99303200-99336400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:99311400-99320800	Weak transcription	Dnd41	blood
5	chr2:99313000-99327000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:99313200-99326600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:99314200-99322000	Enhancers	Fetal Intestine Small	intestine
8	chr2:99315000-99322200	Enhancers	Fetal Intestine Large	intestine
9	chr2:99316000-99320800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr2:99316400-99325000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:99316600-99336400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:99317400-99320600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:99317400-99320600	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:99317400-99321400	Enhancers	Liver	Liver
15	chr2:99317400-99321800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr2:99317600-99321800	Enhancers	Fetal Heart	heart
17	chr2:99317600-99322000	Enhancers	Stomach Mucosa	stomach
18	chr2:99317800-99321000	Enhancers	Fetal Stomach	stomach
19	chr2:99317800-99321600	Enhancers	Brain Hippocampus Middle	brain
20	chr2:99317800-99322800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:99318000-99325200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:99318400-99320600	Enhancers	Fetal Muscle Leg	muscle
23	chr2:99318400-99321200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr2:99318400-99322800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:99318600-99322200	Enhancers	Right Ventricle	heart
26	chr2:99319000-99321600	Weak transcription	Brain Angular Gyrus	brain
27	chr2:99319000-99325400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:99319200-99321600	Weak transcription	Esophagus	oesophagus
29	chr2:99319200-99322000	Enhancers	Primary T cells from cord blood	blood
30	chr2:99319200-99322600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr2:99319200-99323200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr2:99319200-99324000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:99319200-99325000	Weak transcription	Psoas Muscle	Psoas
34	chr2:99319200-99325400	Weak transcription	Aorta	Aorta
35	chr2:99319200-99325400	Weak transcription	Ovary	ovary
36	chr2:99319200-99336800	Weak transcription	Spleen	Spleen
37	chr2:99319400-99321000	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr2:99319400-99324000	Weak transcription	Brain Substantia Nigra	brain
39	chr2:99319600-99321000	Enhancers	Fetal Thymus	thymus
40	chr2:99319600-99321600	Enhancers	HepG2	liver
41	chr2:99319800-99320600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:99319800-99320600	Enhancers	HUVEC	blood vessel
43	chr2:99319800-99320800	Enhancers	Colon Smooth Muscle	Colon
44	chr2:99319800-99320800	Enhancers	Gastric	stomach
45	chr2:99319800-99321000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:99319800-99322000	Enhancers	Left Ventricle	heart
47	chr2:99319800-99322000	Enhancers	Pancreas	Pancrea
48	chr2:99319800-99322000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:99319800-99322200	Enhancers	Right Atrium	heart
50	chr2:99319800-99325400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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