Variant report

Variant	rs530855
Chromosome Location	chr13:76337780-76337781
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17706332	0.85[ASN][1000 genomes]
rs502171	0.80[AFR][1000 genomes]
rs527731	0.84[YRI][hapmap]
rs539514	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625755	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658746	0.81[CEU][hapmap]
rs660942	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs7982226	1.00[JPT][hapmap]
rs7997101	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9544027	1.00[JPT][hapmap]
rs9544064	1.00[JPT][hapmap]
rs9593136	1.00[JPT][hapmap]
rs9600565	1.00[JPT][hapmap]
rs9600566	1.00[JPT][hapmap]
rs9600569	1.00[JPT][hapmap]
rs9600570	1.00[JPT][hapmap]
rs9600576	1.00[JPT][hapmap]

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	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs530855	KCTD12	cis	cerebellum	SCAN
rs530855	COMMD6	cis	cerebellum	SCAN
rs530855	KCTD12	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76308200-76345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:76323800-76356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:76333600-76338800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr13:76333800-76337800	Active TSS	Rectal Smooth Muscle	rectum
5	chr13:76334200-76338200	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr13:76334200-76338400	Active TSS	Duodenum Mucosa	Duodenum
7	chr13:76334400-76338200	Active TSS	Hela-S3	cervix
8	chr13:76334400-76338800	Active TSS	Right Ventricle	heart
9	chr13:76334400-76339600	Active TSS	Fetal Brain Female	brain
10	chr13:76334600-76337800	Active TSS	Brain Anterior Caudate	brain
11	chr13:76334600-76337800	Active TSS	Psoas Muscle	Psoas
12	chr13:76334600-76338000	Active TSS	Fetal Stomach	stomach
13	chr13:76334600-76338200	Active TSS	Fetal Intestine Large	intestine
14	chr13:76334600-76338400	Active TSS	Fetal Intestine Small	intestine
15	chr13:76334800-76343600	Genic enhancers	Osteobl	bone
16	chr13:76335000-76337800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:76335000-76338400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:76335000-76338600	Active TSS	Colonic Mucosa	Colon
19	chr13:76335000-76338600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr13:76335000-76338800	Active TSS	Rectal Mucosa Donor 31	rectum
21	chr13:76335400-76338000	Active TSS	HepG2	liver
22	chr13:76336000-76337800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr13:76336600-76337800	Active TSS	Esophagus	oesophagus
24	chr13:76336600-76338800	Active TSS	Lung	lung
25	chr13:76336600-76339000	Flanking Active TSS	Liver	Liver
26	chr13:76337000-76337800	Active TSS	Aorta	Aorta
27	chr13:76337000-76337800	Active TSS	Fetal Lung	lung
28	chr13:76337000-76338000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr13:76337000-76338000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:76337000-76338400	Weak transcription	Fetal Brain Male	brain
31	chr13:76337000-76338600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:76337000-76338800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:76337000-76338800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:76337000-76339600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr13:76337000-76339800	Weak transcription	NH-A	brain
36	chr13:76337000-76344400	Weak transcription	Ovary	ovary
37	chr13:76337200-76338000	Enhancers	HMEC	breast
38	chr13:76337200-76338400	Weak transcription	Fetal Muscle Leg	muscle
39	chr13:76337200-76338400	Enhancers	HSMMtube	muscle
40	chr13:76337200-76338600	Enhancers	Placenta Amnion	Placenta Amnion
41	chr13:76337200-76338800	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr13:76337200-76338800	Enhancers	Fetal Thymus	thymus
43	chr13:76337200-76339000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr13:76337400-76337800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr13:76337400-76337800	Active TSS	Thymus	Thymus
46	chr13:76337400-76338000	Active TSS	Left Ventricle	heart
47	chr13:76337400-76338000	Enhancers	NHEK	skin
48	chr13:76337400-76338200	Enhancers	GM12878-XiMat	blood
49	chr13:76337400-76338200	Weak transcription	NHDF-Ad	bronchial
50	chr13:76337400-76338400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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