Variant report

Variant	rs12898877
Chromosome Location	chr15:49599256-49599257
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49598053..49600458-chr15:49604572..49606384,3	K562	blood:
2	chr15:49593546..49596024-chr15:49597916..49600433,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11070685	0.89[CEU][hapmap];0.84[CHB][hapmap];0.89[EUR][1000 genomes]
rs12232354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12591799	1.00[YRI][hapmap]
rs12592177	1.00[YRI][hapmap]
rs12592296	1.00[YRI][hapmap]
rs12593068	1.00[YRI][hapmap]
rs12594154	1.00[YRI][hapmap]
rs12594827	1.00[YRI][hapmap]
rs12595497	1.00[YRI][hapmap]
rs12708418	0.80[EUR][1000 genomes]
rs12898461	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903992	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12910584	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.86[ASN][1000 genomes]
rs12914592	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12915792	0.89[CEU][hapmap];0.93[TSI][hapmap]
rs12916078	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13379615	0.80[EUR][1000 genomes]
rs13380075	0.80[EUR][1000 genomes]
rs1429555	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1583060	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs16962414	0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];1.00[MKK][hapmap]
rs16962418	0.89[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs16962419	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs16962434	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34148901	0.81[EUR][1000 genomes]
rs34505850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35001785	0.80[EUR][1000 genomes]
rs35274049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809495	1.00[YRI][hapmap]
rs478500	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs577614	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs6493351	0.86[EUR][1000 genomes]
rs6493366	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[TSI][hapmap]
rs6493367	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[TSI][hapmap]
rs71394957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs71467666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71467668	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71467676	0.81[EUR][1000 genomes]
rs7166491	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169304	0.91[ASN][1000 genomes]
rs7177959	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs8026364	0.95[EUR][1000 genomes]
rs8029538	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036293	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040116	1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[EUR][1000 genomes]
rs9806362	0.95[EUR][1000 genomes]

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	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49557200-49611800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr15:49557800-49607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
4	chr15:49558200-49611800	Weak transcription	Colonic Mucosa	Colon
5	chr15:49561000-49600800	Weak transcription	Pancreas	Pancrea
6	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:49563600-49611000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr15:49565400-49602000	Weak transcription	Fetal Heart	heart
9	chr15:49566200-49611800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:49572800-49600800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:49573600-49613000	Weak transcription	Brain Germinal Matrix	brain
13	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr15:49576600-49605600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr15:49576800-49611800	Weak transcription	Thymus	Thymus
16	chr15:49577000-49605800	Weak transcription	A549	lung
17	chr15:49577200-49607000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:49577600-49605400	Weak transcription	Fetal Intestine Small	intestine
19	chr15:49577800-49611600	Weak transcription	Fetal Brain Female	brain
20	chr15:49578200-49604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:49578200-49611000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:49578400-49605400	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:49578400-49611200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:49579400-49612000	Weak transcription	HUVEC	blood vessel
25	chr15:49580600-49615600	Weak transcription	Fetal Brain Male	brain
26	chr15:49580800-49605600	Weak transcription	NHEK	skin
27	chr15:49581200-49607400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:49581400-49607600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:49582200-49611400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
31	chr15:49583000-49606800	Weak transcription	Fetal Stomach	stomach
32	chr15:49583200-49600800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:49583200-49611400	Weak transcription	Small Intestine	intestine
34	chr15:49583400-49600800	Weak transcription	HSMMtube	muscle
35	chr15:49584000-49605800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:49584000-49607400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:49584000-49607400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:49584800-49600600	Weak transcription	Hela-S3	cervix
39	chr15:49585600-49607200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:49585600-49612800	Weak transcription	Fetal Thymus	thymus
41	chr15:49585800-49600800	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:49586000-49617000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:49586200-49611200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:49588800-49607400	Weak transcription	Brain Substantia Nigra	brain
45	chr15:49588800-49611200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:49588800-49611600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr15:49589200-49607400	Weak transcription	Brain Angular Gyrus	brain
48	chr15:49591400-49600800	Weak transcription	Psoas Muscle	Psoas
49	chr15:49593000-49601400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr15:49593200-49599400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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