Variant report

Variant	rs12464595
Chromosome Location	chr2:55212925-55212926
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	chr2:55205322..55208790-chr2:55211251..55214642,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10170340	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10189379	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10496036	1.00[JPT][hapmap]
rs12464447	0.94[ASN][1000 genomes]
rs12475787	0.92[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12475904	0.91[ASN][1000 genomes]
rs12479297	0.92[ASN][1000 genomes]
rs1348528	0.82[CHB][hapmap]
rs17046570	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17046594	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17347089	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17418675	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1822618	0.82[CHB][hapmap]
rs2864049	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55659423	0.84[ASN][1000 genomes]
rs55698303	0.87[ASN][1000 genomes]
rs56013263	0.89[ASN][1000 genomes]
rs6545467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67156582	0.81[ASN][1000 genomes]
rs6730728	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72795431	0.87[ASN][1000 genomes]
rs72795440	0.92[ASN][1000 genomes]
rs7584354	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7601625	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs887	0.90[JPT][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55193400-55214800	Strong transcription	HepG2	liver
4	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55195000-55215200	Strong transcription	Dnd41	blood
6	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:55196200-55214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
9	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:55198600-55215200	Weak transcription	Lung	lung
13	chr2:55198800-55215200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:55200400-55213400	Weak transcription	Fetal Brain Male	brain
15	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
16	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
17	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
18	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
19	chr2:55204200-55214800	Strong transcription	Fetal Thymus	thymus
20	chr2:55205200-55213400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:55205200-55213600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:55205200-55214600	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:55205200-55214600	Weak transcription	Right Atrium	heart
24	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
25	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
26	chr2:55205600-55214800	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:55205800-55216000	Weak transcription	Fetal Intestine Small	intestine
28	chr2:55206200-55213000	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:55206400-55214800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:55206600-55214000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55206600-55214800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:55206600-55215200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:55206800-55213800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:55206800-55214800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:55207200-55213200	Weak transcription	Fetal Brain Female	brain
36	chr2:55207600-55214800	Strong transcription	K562	blood
37	chr2:55207600-55215200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr2:55207800-55213400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:55207800-55214800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:55207800-55214800	Strong transcription	Fetal Intestine Large	intestine
41	chr2:55207800-55215200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:55208000-55214800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:55208200-55214200	Weak transcription	Brain Germinal Matrix	brain
44	chr2:55208200-55216600	Weak transcription	Stomach Mucosa	stomach
45	chr2:55208400-55214600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:55208400-55215000	Strong transcription	Primary B cells from cord blood	blood
47	chr2:55208600-55214200	Strong transcription	Primary T cells from cord blood	blood
48	chr2:55208800-55213200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr2:55208800-55213200	Weak transcription	Fetal Lung	lung
50	chr2:55208800-55213400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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