Variant report

Variant	rs12296933
Chromosome Location	chr12:46218496-46218497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10161001	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161062	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161510	0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161536	1.00[YRI][hapmap]
rs10506264	0.93[YRI][hapmap]
rs10880858	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11183135	1.00[EUR][1000 genomes]
rs11183136	1.00[EUR][1000 genomes]
rs11183197	1.00[EUR][1000 genomes]
rs11183199	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183202	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183248	0.93[YRI][hapmap]
rs11574971	1.00[YRI][hapmap]
rs12297214	0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301665	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12302862	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs12305110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307979	0.80[YRI][hapmap]
rs12309988	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12316361	0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs12316726	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321106	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28583490	1.00[EUR][1000 genomes]
rs4522236	1.00[EUR][1000 genomes]
rs55916269	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56338250	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58253063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340060	1.00[EUR][1000 genomes]
rs6582575	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7132585	1.00[EUR][1000 genomes]
rs7133123	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296694	0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303119	0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304785	0.82[AFR][1000 genomes]
rs7308856	0.80[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308893	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7309921	0.81[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315365	1.00[EUR][1000 genomes]
rs74081382	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74081384	1.00[EUR][1000 genomes]
rs74081401	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74084208	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953515	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964495	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7965539	1.00[YRI][hapmap]
rs7972499	0.93[YRI][hapmap]
rs7972650	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7973967	0.87[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975170	0.80[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975408	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7977711	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv3325128	chr12:46175148-46224560	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46164600-46230000	Weak transcription	Thymus	Thymus
2	chr12:46177600-46243400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:46182600-46230600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:46183800-46243400	Weak transcription	Small Intestine	intestine
5	chr12:46184600-46231200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:46186000-46233400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:46186800-46243400	Weak transcription	HSMMtube	muscle
8	chr12:46194000-46228200	Weak transcription	Fetal Stomach	stomach
9	chr12:46196400-46243200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:46198000-46229600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:46198200-46226200	Weak transcription	Esophagus	oesophagus
12	chr12:46200600-46244000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:46200800-46227400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:46201800-46233200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:46202200-46233200	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:46202600-46221200	Weak transcription	Fetal Brain Female	brain
17	chr12:46202600-46233400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:46202600-46243400	Weak transcription	Aorta	Aorta
19	chr12:46202800-46220200	Weak transcription	Pancreas	Pancrea
20	chr12:46202800-46230400	Weak transcription	Left Ventricle	heart
21	chr12:46202800-46237800	Weak transcription	Lung	lung
22	chr12:46202800-46243200	Weak transcription	Ovary	ovary
23	chr12:46202800-46243200	Weak transcription	Right Ventricle	heart
24	chr12:46203800-46243800	Weak transcription	Spleen	Spleen
25	chr12:46204000-46230200	Weak transcription	Brain Anterior Caudate	brain
26	chr12:46204000-46233600	Weak transcription	Psoas Muscle	Psoas
27	chr12:46204200-46233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:46205000-46230200	Weak transcription	Osteobl	bone
29	chr12:46205200-46221000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:46205200-46222600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:46205400-46220200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:46205800-46225800	Weak transcription	Brain Germinal Matrix	brain
33	chr12:46207000-46230200	Weak transcription	HMEC	breast
34	chr12:46207400-46244400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr12:46208400-46228200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:46209400-46218600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:46212800-46222200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:46213000-46221000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:46213200-46219600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:46213200-46233200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:46213400-46220600	Strong transcription	Fetal Thymus	thymus
42	chr12:46213600-46221200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:46213800-46228200	Strong transcription	Dnd41	blood
44	chr12:46214000-46219200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:46214200-46218800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:46214200-46222400	Strong transcription	Primary hematopoietic stem cells	blood
47	chr12:46214400-46221600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:46214400-46221600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:46214400-46221600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:46214400-46221800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links