Variant report

Variant	rs56990369
Chromosome Location	chr12:123055140-123055141
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs55817227	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55935830	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56019922	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56977093	0.84[AFR][1000 genomes]
rs57142071	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57766838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58276954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58459934	0.81[AFR][1000 genomes]
rs60586933	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61062446	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61275910	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61585633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6489161	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7134209	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7297776	0.90[AFR][1000 genomes]
rs7307052	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7310898	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7960674	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7972727	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7973067	0.88[AFR][1000 genomes];1.00[AMR][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	nsv899570	chr12:122985057-123089209	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1041677	chr12:122991478-123114125	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	64 gene(s)	inside rSNPs	diseases
3	nsv1054458	chr12:123045662-123133545	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv2761772	chr12:123045674-123115508	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123012400-123066000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:123012400-123114000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:123012400-123117000	Weak transcription	Pancreas	Pancrea
4	chr12:123012400-123121200	Weak transcription	Aorta	Aorta
5	chr12:123012600-123066200	Weak transcription	Psoas Muscle	Psoas
6	chr12:123012600-123095600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:123012800-123065800	Weak transcription	Brain Substantia Nigra	brain
8	chr12:123012800-123097400	Weak transcription	Brain Angular Gyrus	brain
9	chr12:123012800-123109200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:123013000-123076400	Weak transcription	Right Ventricle	heart
11	chr12:123013000-123109200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:123013200-123103000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:123013200-123112400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:123013400-123080600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:123013400-123107400	Weak transcription	Fetal Heart	heart
16	chr12:123013400-123120600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:123014400-123084000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:123014600-123085400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:123015400-123079800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:123015600-123115000	Strong transcription	Dnd41	blood
21	chr12:123022200-123084600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:123022600-123113800	Weak transcription	Colonic Mucosa	Colon
23	chr12:123026000-123076400	Weak transcription	Gastric	stomach
24	chr12:123026000-123081000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:123028600-123064400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:123029200-123085000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:123029200-123107600	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:123032400-123058000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr12:123032600-123095400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:123033400-123067000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:123036400-123074200	Weak transcription	Fetal Brain Male	brain
32	chr12:123037200-123058000	Weak transcription	Left Ventricle	heart
33	chr12:123037200-123113000	Weak transcription	Brain Anterior Caudate	brain
34	chr12:123037600-123057400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:123037600-123095400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:123037800-123100600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:123038000-123059000	Weak transcription	Lung	lung
38	chr12:123038400-123058000	Weak transcription	Spleen	Spleen
39	chr12:123038400-123058800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr12:123038400-123060000	Weak transcription	Fetal Kidney	kidney
41	chr12:123038400-123066200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:123038400-123120000	Weak transcription	Small Intestine	intestine
43	chr12:123041000-123058800	Weak transcription	Esophagus	oesophagus
44	chr12:123042200-123058800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:123042400-123057600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:123042600-123107200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:123042800-123080000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:123043000-123059800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:123043600-123057600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:123043800-123056000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links