Variant report

Variant	rs12906292
Chromosome Location	chr15:49938405-49938406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49936169..49939153-chr15:49946646..49948297,2	K562	blood:
2	chr15:49934440..49937340-chr15:49937772..49940035,3	MCF-7	breast:
3	chr15:49936739..49939305-chr15:49942523..49945381,3	K562	blood:
4	chr15:49914708..49917210-chr15:49937827..49939413,2	MCF-7	breast:
5	chr15:49928084..49930382-chr15:49935420..49939202,4	K562	blood:

Variant related genes	Relation type
ENSG00000261597	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11070712	1.00[AFR][1000 genomes]
rs12324090	0.91[ASN][1000 genomes]
rs12592126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12592839	0.86[ASN][1000 genomes]
rs12594926	0.87[ASN][1000 genomes]
rs12900911	0.91[ASN][1000 genomes]
rs12901023	1.00[AFR][1000 genomes]
rs12901631	1.00[AFR][1000 genomes]
rs12907986	1.00[AFR][1000 genomes]
rs12908295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12909835	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913210	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12913379	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12913571	0.82[ASN][1000 genomes]
rs12913643	1.00[AFR][1000 genomes]
rs12913706	1.00[AFR][1000 genomes]
rs16962583	1.00[AFR][1000 genomes]
rs16962673	1.00[AFR][1000 genomes]
rs2007443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34134305	1.00[AFR][1000 genomes]
rs34212162	0.93[ASN][1000 genomes]
rs34291739	0.87[ASN][1000 genomes]
rs34377746	1.00[AFR][1000 genomes]
rs34461215	0.84[ASN][1000 genomes]
rs34531968	1.00[AFR][1000 genomes]
rs34605270	0.87[ASN][1000 genomes]
rs34737835	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34918968	1.00[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs34951376	1.00[AFR][1000 genomes]
rs34982209	1.00[AFR][1000 genomes]
rs35091054	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35112372	1.00[AFR][1000 genomes]
rs35145376	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35224895	1.00[AFR][1000 genomes]
rs35240887	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs35543719	0.90[ASN][1000 genomes]
rs35563735	1.00[AFR][1000 genomes]
rs35683135	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35699093	1.00[AFR][1000 genomes]
rs35799750	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36048625	0.91[ASN][1000 genomes]
rs36106985	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36114417	1.00[AFR][1000 genomes]
rs4304966	1.00[AFR][1000 genomes]
rs4407014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55662230	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55691379	0.91[ASN][1000 genomes]
rs56053668	0.91[ASN][1000 genomes]
rs56248339	1.00[AFR][1000 genomes]
rs66535408	1.00[AFR][1000 genomes]
rs67031905	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs71467682	1.00[AFR][1000 genomes]
rs71467683	1.00[AFR][1000 genomes]
rs71467692	1.00[AFR][1000 genomes]
rs7175275	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72729117	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs72729172	1.00[AFR][1000 genomes]
rs8025420	0.91[ASN][1000 genomes]
rs8029303	0.90[ASN][1000 genomes]
rs8030269	0.87[ASN][1000 genomes]
rs9972602	0.87[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	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49918000-49938600	Weak transcription	Right Ventricle	heart
2	chr15:49918000-49938800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:49918200-49942200	Weak transcription	GM12878-XiMat	blood
4	chr15:49918600-49938800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:49919800-49940200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:49920000-49940400	Weak transcription	A549	lung
7	chr15:49920800-49940000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:49927000-49940000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:49927600-49938800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:49927800-49938600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:49928000-49940200	Weak transcription	Fetal Intestine Small	intestine
12	chr15:49928200-49939600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:49928200-49940400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:49928200-49940600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:49928200-49943000	Weak transcription	Lung	lung
16	chr15:49928400-49939800	Weak transcription	HUVEC	blood vessel
17	chr15:49929000-49938800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:49930000-49938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:49930400-49939200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:49932400-49939200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:49935600-49938800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:49935600-49939000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:49935600-49939000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:49936000-49939800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:49936200-49939000	Strong transcription	Primary T cells from cord blood	blood
26	chr15:49936200-49939200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:49936400-49938800	Enhancers	Hela-S3	cervix
28	chr15:49936600-49938600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:49936600-49938600	Genic enhancers	NHDF-Ad	bronchial
30	chr15:49936600-49938800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:49936600-49938800	Enhancers	Brain Hippocampus Middle	brain
32	chr15:49936600-49938800	Enhancers	Colon Smooth Muscle	Colon
33	chr15:49936600-49938800	Genic enhancers	Rectal Smooth Muscle	rectum
34	chr15:49936600-49940400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:49936800-49938600	Weak transcription	Placenta	Placenta
36	chr15:49936800-49939000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:49936800-49940600	Weak transcription	Fetal Thymus	thymus
38	chr15:49937000-49938800	Weak transcription	Aorta	Aorta
39	chr15:49937000-49939000	Enhancers	Osteobl	bone
40	chr15:49937000-49939600	Weak transcription	K562	blood
41	chr15:49937000-49939800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr15:49937000-49939800	Weak transcription	Fetal Intestine Large	intestine
43	chr15:49937000-49940000	Weak transcription	Small Intestine	intestine
44	chr15:49937000-49941000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:49937000-49941400	Weak transcription	Brain Germinal Matrix	brain
46	chr15:49937200-49939200	Weak transcription	Primary B cells from cord blood	blood
47	chr15:49937200-49939400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:49937200-49939600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:49937200-49940200	Weak transcription	Dnd41	blood
50	chr15:49937400-49938600	Enhancers	Fetal Kidney	kidney

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