Variant report

Variant	rs579451
Chromosome Location	chr13:30156910-30156911
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30154508..30157101-chr13:30157805..30160613,2	MCF-7	breast:
2	chr13:30156184..30157693-chr13:30157838..30160325,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1018679	0.89[CHB][hapmap]
rs11839516	0.88[ASN][1000 genomes]
rs12428026	0.81[CHB][hapmap]
rs166828	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1877463	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2150688	0.80[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap]
rs2150690	0.81[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap]
rs2236499	0.90[CHB][hapmap]
rs2277451	0.80[CHB][hapmap]
rs2802248	0.81[CHD][hapmap];0.80[GIH][hapmap]
rs2802249	0.81[CHB][hapmap]
rs280922	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs280923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[LWK][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280924	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs280925	0.88[ASN][1000 genomes]
rs280926	0.88[ASN][1000 genomes]
rs280928	0.82[ASN][1000 genomes]
rs280930	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs280931	0.82[ASN][1000 genomes]
rs280933	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs280934	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280936	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2989594	0.81[CHB][hapmap]
rs3011605	0.81[CHB][hapmap]
rs3783257	0.81[CHB][hapmap]
rs3783259	0.81[CHB][hapmap]
rs3783260	0.81[CHB][hapmap]
rs3783262	0.81[CHB][hapmap]
rs3783263	0.81[CHB][hapmap]
rs3803266	0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3825536	0.81[CHB][hapmap]
rs476506	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs485359	0.88[ASN][1000 genomes]
rs532568	0.83[ASN][1000 genomes]
rs537151	0.86[ASN][1000 genomes]
rs617892	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6490409	0.81[CHB][hapmap]
rs7338758	0.85[CHB][hapmap];0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs7991883	0.86[ASN][1000 genomes]
rs7997827	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs819386	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs914362	0.81[CHB][hapmap]
rs9508499	0.83[CHD][hapmap]
rs9550482	0.90[CHB][hapmap]
rs9550483	0.89[ASN][1000 genomes]
rs9551696	0.86[CHB][hapmap]
rs9551699	0.86[CHB][hapmap]
rs9551700	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.87[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	nsv979	chr13:30122254-30167821	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs579451	SHISA2	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30126000-30161400	Weak transcription	Primary B cells from cord blood	blood
2	chr13:30128000-30163600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr13:30128600-30161800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:30128800-30168200	Weak transcription	Primary T cells from cord blood	blood
5	chr13:30138800-30159800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr13:30147200-30163200	Weak transcription	Fetal Intestine Small	intestine
7	chr13:30147800-30163600	Weak transcription	Thymus	Thymus
8	chr13:30148400-30160400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr13:30148400-30167400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr13:30148600-30160800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:30148800-30157400	Weak transcription	GM12878-XiMat	blood
12	chr13:30151600-30157600	Enhancers	Fetal Heart	heart
13	chr13:30152400-30163200	Weak transcription	Spleen	Spleen
14	chr13:30152600-30157800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:30152600-30168200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:30153000-30160800	Weak transcription	HUVEC	blood vessel
17	chr13:30153000-30161200	Weak transcription	Aorta	Aorta
18	chr13:30153200-30157400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:30153200-30161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:30153400-30159200	Weak transcription	Brain Angular Gyrus	brain
21	chr13:30153600-30163200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr13:30153800-30157000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:30153800-30157600	Enhancers	Right Ventricle	heart
24	chr13:30153800-30158200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr13:30154400-30157400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:30154400-30158400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr13:30154400-30158800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr13:30154600-30157200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:30154600-30157600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr13:30154600-30158400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr13:30154600-30160600	Weak transcription	Dnd41	blood
32	chr13:30154600-30163400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:30154800-30157000	Enhancers	NH-A	brain
34	chr13:30154800-30157800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr13:30154800-30159800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:30155000-30157800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr13:30155200-30157800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr13:30155200-30158000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr13:30155200-30158600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr13:30155400-30157400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr13:30155400-30157400	Enhancers	Osteobl	bone
42	chr13:30155400-30157600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr13:30155400-30157600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr13:30155400-30157800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr13:30155400-30157800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr13:30155400-30157800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr13:30155600-30157200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr13:30155600-30157600	Enhancers	Duodenum Mucosa	Duodenum
49	chr13:30155600-30157600	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr13:30155600-30157800	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links