Variant report

Variant	rs2017594
Chromosome Location	chr12:122631208-122631209
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122627308..122628823-chr12:122630671..122632558,2	MCF-7	breast:
2	chr12:122471389..122473549-chr12:122630126..122632348,2	K562	blood:
3	chr12:122513440..122515141-chr12:122630792..122633616,2	K562	blood:
4	chr12:122623410..122625195-chr12:122629931..122632295,2	K562	blood:
5	chr12:122623695..122625503-chr12:122629931..122631877,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1043763	0.89[EUR][1000 genomes]
rs1043764	0.89[EUR][1000 genomes]
rs10847689	0.94[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11057403	0.87[EUR][1000 genomes]
rs11057509	0.81[ASN][1000 genomes]
rs11061153	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12299752	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28478029	0.87[EUR][1000 genomes]
rs28622891	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28707600	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36045144	0.92[EUR][1000 genomes]
rs3741452	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4075625	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4132932	0.87[EUR][1000 genomes]
rs4132933	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4758689	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73217773	0.87[EUR][1000 genomes]
rs73219860	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9668430	0.94[CEU][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.96[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2017594	VSIG10	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122608600-122632800	Strong transcription	Fetal Stomach	stomach
2	chr12:122610600-122633200	Weak transcription	Right Atrium	heart
3	chr12:122612000-122632400	Strong transcription	Fetal Intestine Small	intestine
4	chr12:122612200-122632400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr12:122616000-122631600	Weak transcription	Fetal Brain Male	brain
6	chr12:122616200-122632600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:122627000-122646800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:122627400-122636400	Weak transcription	K562	blood
9	chr12:122627600-122633800	Weak transcription	Primary B cells from cord blood	blood
10	chr12:122627800-122636000	Weak transcription	Psoas Muscle	Psoas
11	chr12:122628000-122633400	Weak transcription	Small Intestine	intestine
12	chr12:122628200-122631600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:122628200-122633400	Weak transcription	Stomach Mucosa	stomach
14	chr12:122628200-122633800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:122628200-122637400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:122628400-122631800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:122628400-122636400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:122628600-122632800	Weak transcription	Placenta	Placenta
19	chr12:122628600-122633200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:122628600-122633400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:122628600-122640000	Weak transcription	Esophagus	oesophagus
22	chr12:122628800-122631800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:122628800-122631800	Weak transcription	Brain Germinal Matrix	brain
24	chr12:122628800-122632800	Weak transcription	Fetal Brain Female	brain
25	chr12:122628800-122632800	Weak transcription	NHLF	lung
26	chr12:122628800-122633000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:122628800-122633000	Weak transcription	Fetal Lung	lung
28	chr12:122628800-122633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:122628800-122633400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:122628800-122633600	Weak transcription	Adipose Nuclei	Adipose
31	chr12:122628800-122633800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:122628800-122636200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:122628800-122636200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:122628800-122636200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:122628800-122636400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr12:122628800-122636400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:122628800-122636400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:122628800-122636600	Weak transcription	A549	lung
39	chr12:122628800-122637400	Weak transcription	Brain Anterior Caudate	brain
40	chr12:122628800-122637600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr12:122629000-122636600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:122629200-122631400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:122629200-122632200	Weak transcription	Fetal Thymus	thymus
44	chr12:122629200-122632800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:122629200-122633000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:122629200-122633200	Weak transcription	Osteobl	bone
47	chr12:122629200-122633400	Weak transcription	Ovary	ovary
48	chr12:122629200-122633600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:122629200-122640600	Weak transcription	Primary T cells from cord blood	blood
50	chr12:122629200-122643600	Weak transcription	Colon Smooth Muscle	Colon

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