Variant report

Variant	rs13005519
Chromosome Location	chr2:152677355-152677356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10171724	0.83[AFR][1000 genomes]
rs10184063	0.82[AFR][1000 genomes]
rs11680834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11682909	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs11894672	0.90[YRI][hapmap];0.82[AFR][1000 genomes]
rs1523181	0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs1568673	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2030588	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs2293220	1.00[CEU][hapmap]
rs2293221	0.82[AFR][1000 genomes]
rs3768658	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs3820705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664066	0.81[YRI][hapmap]
rs6433656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7609344	0.82[EUR][1000 genomes];0.92[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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693430	chr2:152648677-152681200	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152619000-152677400	Weak transcription	Brain Substantia Nigra	brain
2	chr2:152623000-152680000	Weak transcription	Spleen	Spleen
3	chr2:152632200-152679200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:152634000-152683400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:152643400-152679000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:152649000-152680200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:152654200-152683400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:152654400-152678000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:152654400-152679000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:152658000-152681600	Weak transcription	Stomach Mucosa	stomach
11	chr2:152659400-152683000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:152661400-152683000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:152662200-152681000	Weak transcription	Colonic Mucosa	Colon
14	chr2:152662800-152683000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:152663200-152680000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:152663400-152682200	Weak transcription	HSMMtube	muscle
17	chr2:152663400-152683000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:152664600-152679400	Weak transcription	Osteobl	bone
19	chr2:152665600-152679600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:152667800-152680000	Weak transcription	NHLF	lung
21	chr2:152667800-152682400	Weak transcription	Fetal Brain Male	brain
22	chr2:152668000-152678800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:152668400-152680000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:152668400-152683200	Weak transcription	Small Intestine	intestine
25	chr2:152668600-152679200	Weak transcription	A549	lung
26	chr2:152668800-152679200	Weak transcription	Brain Germinal Matrix	brain
27	chr2:152668800-152679200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:152668800-152680200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:152669600-152679200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:152669800-152683200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:152670000-152680200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:152670200-152683200	Weak transcription	Fetal Kidney	kidney
33	chr2:152670400-152680200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:152670400-152681000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr2:152670400-152681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:152670600-152679200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:152670600-152680400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:152670600-152682800	Weak transcription	HMEC	breast
39	chr2:152670800-152680000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr2:152670800-152680000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr2:152670800-152682800	Weak transcription	Hela-S3	cervix
42	chr2:152671000-152679000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:152671000-152679000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:152671000-152679200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:152671000-152679400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:152671000-152679800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr2:152671000-152680000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:152671000-152680200	Weak transcription	Brain Angular Gyrus	brain
49	chr2:152671000-152681200	Weak transcription	Liver	Liver
50	chr2:152671000-152682800	Weak transcription	NH-A	brain

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