Variant report

Variant	rs60056536
Chromosome Location	chr12:50600130-50600131
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF1	chr12:50600080-50600233	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50597958..50602856-chr12:50604694..50610518,6	K562	blood:
2	chr12:50592640..50596172-chr12:50599889..50601939,3	MCF-7	breast:
3	chr12:50596667..50602931-chr12:50613575..50616735,6	K562	blood:
4	chr12:50598358..50601280-chr12:50607490..50609263,3	K562	blood:

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000050405	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs61255936	1.00[AFR][1000 genomes]
rs74090081	1.00[AFR][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
5	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
6	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
7	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
9	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
10	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:50588400-50600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:50588400-50600600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:50588400-50600600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr12:50589400-50600800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:50590600-50600200	Strong transcription	Fetal Thymus	thymus
17	chr12:50591000-50600200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:50591000-50603000	Strong transcription	Fetal Muscle Trunk	muscle
19	chr12:50591600-50615600	Weak transcription	HepG2	liver
20	chr12:50592000-50600200	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:50593400-50614200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:50593400-50614200	Weak transcription	Fetal Brain Male	brain
23	chr12:50593400-50614600	Weak transcription	Esophagus	oesophagus
24	chr12:50595600-50600600	Strong transcription	Primary T cells from cord blood	blood
25	chr12:50595800-50600800	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:50596200-50613400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr12:50596400-50600600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:50596400-50600800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:50596600-50600600	Strong transcription	HSMMtube	muscle
30	chr12:50596600-50604600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:50596600-50605400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:50596600-50607200	Strong transcription	Fetal Intestine Small	intestine
33	chr12:50596800-50600800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:50596800-50601400	Strong transcription	HSMM	muscle
35	chr12:50596800-50604200	Strong transcription	Fetal Stomach	stomach
36	chr12:50596800-50607600	Weak transcription	Stomach Mucosa	stomach
37	chr12:50596800-50614000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr12:50597000-50602400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:50597000-50603200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr12:50597000-50604600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:50597200-50600400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:50597200-50600400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr12:50597200-50600800	Strong transcription	NHLF	lung
44	chr12:50597200-50604200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr12:50597600-50600200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:50597600-50600400	Genic enhancers	HMEC	breast
47	chr12:50597600-50600600	Strong transcription	Colonic Mucosa	Colon
48	chr12:50597600-50600600	Strong transcription	Fetal Lung	lung
49	chr12:50597600-50601800	Strong transcription	NHDF-Ad	bronchial
50	chr12:50597800-50600800	Strong transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links