Variant report

Variant	rs280934
Chromosome Location	chr13:30155020-30155021
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:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1018679	0.89[CHB][hapmap]
rs11839516	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12428026	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs166828	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1877463	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2150688	0.80[CHB][hapmap]
rs2150690	0.81[CHB][hapmap]
rs2236499	0.90[CHB][hapmap]
rs2277451	0.80[CHB][hapmap]
rs2802249	0.81[CHB][hapmap]
rs280922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs280923	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs280924	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs280925	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs280926	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs280928	0.94[ASN][1000 genomes]
rs280930	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs280931	0.93[ASN][1000 genomes]
rs280933	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs280936	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2989594	0.81[CHB][hapmap]
rs3011605	0.81[CHB][hapmap]
rs3783257	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs3783259	0.81[CHB][hapmap]
rs3783260	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs3783262	0.81[CHB][hapmap]
rs3783263	0.81[CHB][hapmap]
rs3803266	0.85[CHB][hapmap]
rs3825536	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs476506	1.00[CHB][hapmap]
rs485359	0.99[ASN][1000 genomes]
rs532568	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs537151	0.97[ASN][1000 genomes]
rs579451	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]
rs617892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6490409	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs7338758	0.85[CHB][hapmap]
rs7991883	0.97[ASN][1000 genomes]
rs7997827	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs819386	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914362	0.81[CHB][hapmap]
rs9550482	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs9551696	0.86[CHB][hapmap]
rs9551699	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9551700	0.86[CHB][hapmap]
rs9551701	0.90[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
rs280934	SHISA2	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30126000-30161400	Weak transcription	Primary B cells from cord blood	blood
2	chr13:30127600-30156400	Weak transcription	Lung	lung
3	chr13:30128000-30163600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr13:30128600-30161800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:30128800-30155800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr13:30128800-30168200	Weak transcription	Primary T cells from cord blood	blood
7	chr13:30138800-30155800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr13:30138800-30159800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:30144400-30155600	Weak transcription	HMEC	breast
10	chr13:30146400-30155400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:30147200-30163200	Weak transcription	Fetal Intestine Small	intestine
12	chr13:30147600-30155400	Weak transcription	Fetal Brain Male	brain
13	chr13:30147800-30155200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr13:30147800-30155600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:30147800-30163600	Weak transcription	Thymus	Thymus
16	chr13:30148200-30155600	Weak transcription	Ovary	ovary
17	chr13:30148200-30156400	Weak transcription	Stomach Mucosa	stomach
18	chr13:30148200-30156600	Weak transcription	A549	lung
19	chr13:30148200-30156800	Weak transcription	NHLF	lung
20	chr13:30148400-30155800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr13:30148400-30160400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr13:30148400-30167400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr13:30148600-30155600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:30148600-30156000	Weak transcription	Small Intestine	intestine
25	chr13:30148600-30160800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:30148800-30157400	Weak transcription	GM12878-XiMat	blood
27	chr13:30149200-30155600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:30150800-30155800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:30151600-30156000	Weak transcription	Fetal Stomach	stomach
30	chr13:30151600-30156800	Enhancers	Colon Smooth Muscle	Colon
31	chr13:30151600-30157600	Enhancers	Fetal Heart	heart
32	chr13:30152200-30155800	Weak transcription	Gastric	stomach
33	chr13:30152400-30163200	Weak transcription	Spleen	Spleen
34	chr13:30152600-30157800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:30152600-30168200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:30152800-30155800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr13:30153000-30160800	Weak transcription	HUVEC	blood vessel
38	chr13:30153000-30161200	Weak transcription	Aorta	Aorta
39	chr13:30153200-30155400	Weak transcription	Brain Substantia Nigra	brain
40	chr13:30153200-30155400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr13:30153200-30155600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:30153200-30155600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr13:30153200-30155600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr13:30153200-30155600	Weak transcription	NHDF-Ad	bronchial
45	chr13:30153200-30155800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr13:30153200-30156000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:30153200-30156800	Weak transcription	HSMMtube	muscle
48	chr13:30153200-30157400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr13:30153200-30161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:30153400-30155200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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