Variant report

Variant	rs1560761
Chromosome Location	chr12:106477437-106477438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10492351	0.82[JPT][hapmap]
rs10746054	0.88[CEU][hapmap]
rs12318540	0.82[JPT][hapmap]
rs1427793	0.82[JPT][hapmap]
rs1896364	0.82[JPT][hapmap];0.81[LWK][hapmap]
rs2436595	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs892270	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832509	chr12:106363888-106516221	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1560761	SLC41A2	cis	parietal	SCAN
rs1560761	CKAP4	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106458800-106500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:106461800-106499600	Weak transcription	Fetal Intestine Large	intestine
3	chr12:106462400-106482600	Weak transcription	Esophagus	oesophagus
4	chr12:106463800-106477600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:106465200-106487000	Weak transcription	Brain Germinal Matrix	brain
6	chr12:106466200-106477600	Genic enhancers	HSMM	muscle
7	chr12:106467000-106477600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:106469000-106490200	Weak transcription	Gastric	stomach
9	chr12:106469000-106499400	Weak transcription	Fetal Intestine Small	intestine
10	chr12:106469200-106477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:106471400-106477600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:106471400-106478400	Enhancers	Right Atrium	heart
13	chr12:106472000-106477600	Enhancers	NHLF	lung
14	chr12:106472000-106478400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:106472200-106477800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:106472200-106477800	Genic enhancers	A549	lung
17	chr12:106472200-106478000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:106472400-106478000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:106472400-106479400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:106472600-106477600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:106472800-106480400	Weak transcription	Pancreas	Pancrea
22	chr12:106472800-106480600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:106473000-106482000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:106473400-106477600	Strong transcription	Fetal Brain Female	brain
25	chr12:106474600-106478000	Weak transcription	Fetal Lung	lung
26	chr12:106474600-106480000	Enhancers	NHDF-Ad	bronchial
27	chr12:106474600-106484600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:106474800-106478200	Strong transcription	Liver	Liver
29	chr12:106474800-106479800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:106475000-106477600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:106475000-106482400	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:106475200-106478600	Genic enhancers	Left Ventricle	heart
33	chr12:106475400-106477600	Strong transcription	Fetal Stomach	stomach
34	chr12:106475400-106477800	Genic enhancers	Brain Anterior Caudate	brain
35	chr12:106475400-106482200	Weak transcription	Psoas Muscle	Psoas
36	chr12:106475600-106477800	Genic enhancers	Brain Angular Gyrus	brain
37	chr12:106475800-106477600	Genic enhancers	Brain Inferior Temporal Lobe	brain
38	chr12:106475800-106484200	Weak transcription	Hela-S3	cervix
39	chr12:106476000-106477800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:106476000-106477800	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:106476200-106477800	Weak transcription	Ovary	ovary
42	chr12:106476200-106477800	Strong transcription	NHEK	skin
43	chr12:106476200-106479400	Enhancers	Fetal Heart	heart
44	chr12:106476400-106477800	Transcr. at gene 5' and 3'	HSMMtube	muscle
45	chr12:106476400-106478000	Genic enhancers	Osteobl	bone
46	chr12:106476400-106478400	Genic enhancers	Right Ventricle	heart
47	chr12:106476400-106479400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:106476600-106477600	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr12:106476600-106477800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:106476600-106483200	Weak transcription	Fetal Brain Male	brain

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