Variant report

Variant	rs9558
Chromosome Location	chr2:30481917-30481918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30481283..30483299-chr2:30485255..30486981,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YPEL5-5	chr2:30481193-30482893	NONHSAT069896

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1001204	0.95[EUR][1000 genomes]
rs10171296	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1039835	1.00[CHB][hapmap]
rs1039836	1.00[CHB][hapmap]
rs10495774	0.81[MEX][hapmap]
rs11127264	1.00[CHB][hapmap]
rs11678385	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12467407	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs13386455	1.00[CEU][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs13389106	0.89[EUR][1000 genomes]
rs17009304	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17009315	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17321999	1.00[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs1962588	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2089657	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs3817143	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952115	1.00[CEU][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs57667995	0.82[ASN][1000 genomes]
rs59693338	0.90[EUR][1000 genomes]
rs6548005	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6708792	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs6732241	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6733372	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs72787716	0.88[EUR][1000 genomes]
rs72787719	0.91[EUR][1000 genomes]
rs72787721	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787722	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72787724	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73925103	0.91[EUR][1000 genomes]
rs7604484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906865	0.95[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs906867	1.00[CEU][hapmap];0.81[TSI][hapmap];0.95[EUR][1000 genomes]
rs9309678	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967884	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv2662	chr2:30462905-30495134	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9558	PLB1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30471000-30484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:30471200-30482000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:30472600-30483400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:30476200-30483400	Weak transcription	Brain Anterior Caudate	brain
5	chr2:30476600-30496000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:30476800-30485600	Weak transcription	Fetal Kidney	kidney
7	chr2:30477000-30484200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:30477000-30488800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:30477200-30483800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr2:30477600-30483600	Strong transcription	Fetal Stomach	stomach
11	chr2:30477800-30482800	Strong transcription	Aorta	Aorta
12	chr2:30477800-30489000	Weak transcription	Stomach Mucosa	stomach
13	chr2:30478000-30482400	Genic enhancers	Left Ventricle	heart
14	chr2:30478000-30488400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:30478200-30488400	Weak transcription	Right Atrium	heart
16	chr2:30478600-30487400	Weak transcription	K562	blood
17	chr2:30478800-30484000	Strong transcription	NHLF	lung
18	chr2:30479000-30482600	Strong transcription	Lung	lung
19	chr2:30479000-30483000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:30479000-30483400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:30479000-30483400	Strong transcription	Stomach Smooth Muscle	stomach
22	chr2:30479000-30483600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:30479200-30482200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:30479200-30484000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:30479200-30484000	Strong transcription	HSMMtube	muscle
26	chr2:30479200-30489000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:30479400-30482200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:30479400-30482400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:30479400-30482800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:30479400-30483400	Strong transcription	Osteobl	bone
31	chr2:30479400-30483600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:30479400-30484000	Strong transcription	Primary B cells from cord blood	blood
33	chr2:30479400-30484000	Strong transcription	HSMM	muscle
34	chr2:30479600-30482000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
35	chr2:30479600-30482200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:30479600-30482400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr2:30479600-30482400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:30479600-30482800	Strong transcription	NH-A	brain
39	chr2:30479600-30483200	Genic enhancers	Fetal Heart	heart
40	chr2:30479600-30483600	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:30479600-30483800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:30479600-30483800	Strong transcription	Fetal Brain Female	brain
43	chr2:30479600-30484000	Strong transcription	Fetal Lung	lung
44	chr2:30479800-30482200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:30479800-30482400	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:30479800-30484000	Strong transcription	NHDF-Ad	bronchial
47	chr2:30480000-30482000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:30480000-30483000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:30480200-30482600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:30480200-30482600	Strong transcription	Placenta	Placenta

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