Variant report

Variant	rs966477
Chromosome Location	chr2:86737649-86737650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86735334..86737957-chr2:86740188..86742060,2	K562	blood:
2	chr2:86736546..86738980-chr2:86748664..86751290,2	K562	blood:
3	chr2:86737238..86738787-chr2:86945375..86947956,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153561	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10185085	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1036940	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs11127040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11127042	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1116326	0.91[ASN][1000 genomes]
rs11693352	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11903855	1.00[CHB][hapmap]
rs12476666	0.81[ASN][1000 genomes]
rs12623509	0.83[GIH][hapmap]
rs12714185	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12714187	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12995117	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs1468039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1518811	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17027280	0.83[LWK][hapmap]
rs2030259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2044230	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2139150	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs218060	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2367575	1.00[ASN][1000 genomes]
rs308901	0.87[CHD][hapmap]
rs308907	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs308913	1.00[JPT][hapmap]
rs396354	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs433655	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4832285	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4832289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4832290	0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs4832293	1.00[ASN][1000 genomes]
rs4832294	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs4832298	0.80[ASN][1000 genomes]
rs6547688	0.81[ASN][1000 genomes]
rs6547689	0.81[ASN][1000 genomes]
rs6547690	0.81[ASN][1000 genomes]
rs6547700	0.87[CHD][hapmap];0.81[GIH][hapmap]
rs6710124	1.00[CHB][hapmap]
rs6714826	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs6714957	0.80[ASN][1000 genomes]
rs6742018	1.00[JPT][hapmap]
rs683139	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs7562493	0.81[LWK][hapmap]
rs7574389	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7598058	0.81[ASN][1000 genomes]
rs950780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs966477	MAT2A	cis	parietal	SCAN
rs966477	RNF103	cis	cerebellum	SCAN
rs966477	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs966477	VPS24	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
3	chr2:86726400-86741800	Weak transcription	NH-A	brain
4	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
6	chr2:86726800-86739000	Weak transcription	K562	blood
7	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:86728000-86737800	Strong transcription	Fetal Intestine Large	intestine
10	chr2:86728000-86738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr2:86728000-86738400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:86728200-86737800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr2:86728200-86737800	Weak transcription	Stomach Mucosa	stomach
14	chr2:86728200-86738400	Strong transcription	Dnd41	blood
15	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
16	chr2:86728400-86737800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:86728400-86738000	Strong transcription	Liver	Liver
18	chr2:86728400-86738400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:86728400-86738400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:86728400-86738400	Strong transcription	A549	lung
21	chr2:86728400-86747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:86728600-86738200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:86728600-86738800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:86728800-86737800	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:86728800-86737800	Strong transcription	Placenta	Placenta
26	chr2:86729000-86737800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:86729000-86738000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr2:86729000-86738000	Strong transcription	Thymus	Thymus
29	chr2:86729000-86738200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:86729000-86738400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr2:86729000-86738600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:86729000-86747000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:86729200-86737800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:86729200-86738600	Strong transcription	Primary T cells from cord blood	blood
35	chr2:86729400-86738000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr2:86729400-86738400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:86729600-86737800	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:86729600-86738200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:86729600-86738200	Strong transcription	Fetal Thymus	thymus
40	chr2:86729600-86738400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:86729800-86738000	Strong transcription	HepG2	liver
42	chr2:86729800-86738200	Strong transcription	Primary B cells from cord blood	blood
43	chr2:86730000-86737800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:86730200-86738200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:86730600-86739000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:86730800-86737800	Strong transcription	Lung	lung
47	chr2:86731000-86737800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:86731600-86737800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:86731600-86737800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:86732000-86738000	Strong transcription	Fetal Intestine Small	intestine

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