Variant report

Variant	rs2279740
Chromosome Location	chr12:64586309-64586310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64584927..64586480-chr12:64615243..64617151,2	K562	blood:
2	chr12:64584185..64586807-chr12:64797438..64799794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243024	Chromatin interaction
ENSG00000184575	Chromatin interaction
ENSG00000174206	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1002392	0.82[CHB][hapmap]
rs10784390	0.81[CHB][hapmap]
rs10784392	0.81[CHB][hapmap]
rs10784394	0.82[CHB][hapmap]
rs10784397	0.82[CHB][hapmap]
rs10878128	0.82[CHB][hapmap]
rs10878129	0.81[CHB][hapmap]
rs10878130	0.82[CHB][hapmap]
rs10878131	0.82[CHB][hapmap]
rs10878134	0.82[CHB][hapmap]
rs11175307	0.82[CHB][hapmap]
rs1162974	0.82[CHB][hapmap]
rs1162976	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs1162977	0.82[CHB][hapmap]
rs1178702	0.81[CHB][hapmap]
rs1178703	0.85[CHB][hapmap]
rs1185525	0.81[CHB][hapmap]
rs12309193	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs12581277	0.82[JPT][hapmap]
rs12581905	0.82[CHB][hapmap]
rs1695105	0.87[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs17100184	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1865791	0.81[CHB][hapmap]
rs1865798	0.82[CHB][hapmap]
rs1898220	0.81[CHB][hapmap]
rs2010893	0.82[CHB][hapmap]
rs2647911	0.84[CHD][hapmap]
rs4763009	0.85[CHB][hapmap]
rs4763010	0.82[CHB][hapmap]
rs4763144	0.82[CHB][hapmap]
rs4763145	0.82[CHB][hapmap]
rs4763146	0.82[CHB][hapmap]
rs4763147	0.82[CHB][hapmap]
rs5015817	0.82[CHB][hapmap]
rs5015818	0.82[CHB][hapmap]
rs6581534	0.82[CHB][hapmap]
rs7306905	0.82[CHB][hapmap]
rs789721	0.87[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs789749	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs789750	0.83[ASN][1000 genomes]
rs7956726	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs9705644	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9804707	0.95[CHB][hapmap];1.00[JPT][hapmap]

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	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3509287	chr12:64526217-64736995	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3509288	chr12:64526217-64736995	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64574600-64587600	Weak transcription	Left Ventricle	heart
2	chr12:64574600-64597000	Weak transcription	Esophagus	oesophagus
3	chr12:64574800-64586400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:64575000-64615200	Weak transcription	Psoas Muscle	Psoas
5	chr12:64575200-64597000	Weak transcription	Aorta	Aorta
6	chr12:64575400-64587600	Weak transcription	Spleen	Spleen
7	chr12:64575400-64590400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:64575600-64586800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:64575600-64587400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:64575600-64587600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:64575600-64607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:64575600-64615000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:64575800-64615200	Weak transcription	Fetal Stomach	stomach
14	chr12:64576000-64587400	Weak transcription	Brain Anterior Caudate	brain
15	chr12:64576000-64587600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:64576000-64587800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:64576000-64597200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:64576000-64615000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:64576200-64586600	Weak transcription	Brain Substantia Nigra	brain
20	chr12:64576200-64586800	Weak transcription	Liver	Liver
21	chr12:64576200-64587400	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:64576200-64587800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:64576200-64589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:64576400-64587400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:64576600-64587400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr12:64581200-64587400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:64581200-64587600	Weak transcription	HSMM	muscle
28	chr12:64581200-64587800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:64581200-64597000	Weak transcription	HSMMtube	muscle
30	chr12:64581400-64586600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:64581400-64586800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:64581400-64587400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:64581400-64614600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:64581600-64589000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:64581800-64587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:64581800-64588600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:64581800-64615400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:64582000-64586600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:64582000-64586800	Weak transcription	Adipose Nuclei	Adipose
40	chr12:64582000-64587400	Weak transcription	HMEC	breast
41	chr12:64582000-64587600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:64582200-64587400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr12:64582400-64586800	Weak transcription	NHEK	skin
44	chr12:64582400-64587200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:64582400-64587400	Weak transcription	Osteobl	bone
46	chr12:64582400-64588800	Weak transcription	NHLF	lung
47	chr12:64582600-64587000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:64582600-64587600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:64582600-64587600	Weak transcription	A549	lung
50	chr12:64582600-64587800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links