Variant report

Variant	rs4575769
Chromosome Location	chr2:46976834-46976835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46965000..46967486-chr2:46976098..46978644,2	K562	blood:
2	chr2:46969632..46972292-chr2:46976605..46978764,2	K562	blood:
3	chr2:46930029..46933528-chr2:46976256..46980348,3	K562	blood:
4	chr2:46976318..46977932-chr2:46979350..46982138,4	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10495938	0.80[AFR][1000 genomes]
rs11889273	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892177	0.89[AFR][1000 genomes]
rs11892710	0.85[AFR][1000 genomes]
rs11893159	0.82[YRI][hapmap]
rs11893443	0.89[AFR][1000 genomes]
rs11893955	0.83[AFR][1000 genomes]
rs11903382	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17771005	1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17771237	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17771255	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17771357	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17772309	0.81[AFR][1000 genomes]
rs17822668	0.95[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17822704	0.96[AFR][1000 genomes]
rs41320947	0.89[AFR][1000 genomes]
rs41349351	0.89[AFR][1000 genomes]
rs41370847	0.83[AFR][1000 genomes]
rs41375646	0.91[AFR][1000 genomes]
rs41379147	0.89[AFR][1000 genomes]
rs41432848	0.89[AFR][1000 genomes]
rs41478946	0.89[AFR][1000 genomes]
rs56953385	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62134765	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6731970	0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6735101	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6749450	0.87[AFR][1000 genomes]
rs72802460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72802489	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591613	0.91[AFR][1000 genomes]
rs7606134	0.82[AFR][1000 genomes]
rs9677272	1.00[CEU][hapmap];0.82[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9677705	1.00[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv3459561	chr2:46967674-46979121	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3459562	chr2:46967674-46979121	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	esv14887	chr2:46967820-46978960	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	esv2760650	chr2:46970686-46978878	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4575769	PLEKHH2	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:46948200-46977200	Weak transcription	Aorta	Aorta
3	chr2:46955200-46984800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:46955200-46985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr2:46956000-46980000	Weak transcription	Right Atrium	heart
6	chr2:46960000-46978800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:46960000-46988000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:46962000-46982000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:46964800-46985800	Weak transcription	Primary B cells from cord blood	blood
10	chr2:46965400-46979200	Weak transcription	Psoas Muscle	Psoas
11	chr2:46965600-46980800	Weak transcription	Fetal Heart	heart
12	chr2:46965800-46986800	Weak transcription	Hela-S3	cervix
13	chr2:46968000-46979200	Weak transcription	Left Ventricle	heart
14	chr2:46968000-46980000	Weak transcription	Spleen	Spleen
15	chr2:46969400-46988200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:46972600-46977400	Enhancers	NHLF	lung
17	chr2:46972600-46981000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:46972600-46986600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:46973200-46981400	Enhancers	NHDF-Ad	bronchial
20	chr2:46973400-46985600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:46973600-46980000	Enhancers	Osteobl	bone
22	chr2:46974200-46983000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:46974400-46977000	Enhancers	Colon Smooth Muscle	Colon
24	chr2:46974400-46977200	Enhancers	HMEC	breast
25	chr2:46974400-46977400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:46974400-46977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:46974400-46977400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:46974400-46977400	Enhancers	Fetal Stomach	stomach
29	chr2:46974400-46980000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:46974600-46977000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr2:46974600-46990000	Weak transcription	Colonic Mucosa	Colon
32	chr2:46974800-46977400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:46974800-46980200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:46974800-46985600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:46974800-46986600	Weak transcription	Gastric	stomach
36	chr2:46975000-46979000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:46975000-46979200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:46975000-46979200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:46975000-46980400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:46975000-46985400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:46975000-46986800	Weak transcription	GM12878-XiMat	blood
42	chr2:46975200-46977200	Enhancers	HepG2	liver
43	chr2:46975200-46979000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:46975600-46985400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:46975600-46985400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr2:46975600-46985400	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:46975600-46985400	Weak transcription	Lung	lung
48	chr2:46975600-46986000	Weak transcription	Esophagus	oesophagus
49	chr2:46975600-46986400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:46975800-46977400	Enhancers	Duodenum Smooth Muscle	Duodenum

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