Variant report

Variant	rs10746024
Chromosome Location	chr12:105776494-105776495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1061749	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10735403	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10735404	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10778394	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10861405	0.86[JPT][hapmap]
rs10861406	0.83[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10861408	0.82[ASN][1000 genomes]
rs10861416	0.87[ASN][1000 genomes]
rs11112491	0.83[ASN][1000 genomes]
rs1432588	0.83[ASN][1000 genomes]
rs2116675	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6539209	0.92[ASN][1000 genomes]
rs7960794	0.86[ASN][1000 genomes]
rs7962661	0.83[ASN][1000 genomes]
rs8181638	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs941107	0.94[ASN][1000 genomes]
rs9988966	0.83[ASN][1000 genomes]
rs9989027	0.82[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.83[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	nsv899500	chr12:105742674-105803028	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10746024	BTBD11	cis	cerebellum	SCAN
rs10746024	SYCP3	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105734800-105776600	Weak transcription	Esophagus	oesophagus
2	chr12:105735000-105776600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:105735600-105776600	Weak transcription	Fetal Intestine Small	intestine
4	chr12:105746000-105776800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:105748000-105776600	Weak transcription	Gastric	stomach
6	chr12:105748800-105776800	Weak transcription	Pancreas	Pancrea
7	chr12:105751200-105776800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:105760000-105776600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:105762800-105776800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:105763000-105776600	Weak transcription	Fetal Kidney	kidney
11	chr12:105763000-105776800	Weak transcription	Fetal Intestine Large	intestine
12	chr12:105764800-105803600	Weak transcription	Thymus	Thymus
13	chr12:105765000-105776800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:105766400-105777000	Weak transcription	GM12878-XiMat	blood
15	chr12:105766600-105776600	Weak transcription	HMEC	breast
16	chr12:105767200-105776600	Weak transcription	Fetal Stomach	stomach
17	chr12:105767400-105776600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:105767400-105776800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:105768400-105776600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:105768800-105776600	Weak transcription	NHEK	skin
21	chr12:105768800-105776800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:105769000-105776800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:105769000-105778400	Weak transcription	Dnd41	blood
24	chr12:105769400-105776600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:105769400-105776800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:105773200-105776800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:105773400-105776600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:105773400-105776600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:105773400-105776600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:105773600-105776600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:105775000-105776600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:105775400-105776800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:105775600-105776600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:105775600-105776800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:105776200-105776600	Enhancers	Stomach Mucosa	stomach
36	chr12:105776200-105776800	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr12:105776200-105777400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:105776400-105776600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:105776400-105776600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:105776400-105776600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:105776400-105776600	Bivalent Enhancer	Adipose Nuclei	Adipose
42	chr12:105776400-105776600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr12:105776400-105776600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr12:105776400-105776600	Enhancers	NHLF	lung
45	chr12:105776400-105776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:105776400-105776800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:105776400-105776800	Enhancers	Brain Hippocampus Middle	brain
48	chr12:105776400-105776800	Enhancers	Fetal Lung	lung
49	chr12:105776400-105776800	Enhancers	Fetal Muscle Leg	muscle
50	chr12:105776400-105776800	Enhancers	Rectal Smooth Muscle	rectum

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