Variant report

Variant	rs10497524
Chromosome Location	chr2:179661853-179661854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10497522	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10497525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11887915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11892354	0.94[ASN][1000 genomes]
rs11897386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11904138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12693168	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1552280	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1872202	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs1905521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2035496	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2046778	0.90[CHB][hapmap]
rs2054706	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2054707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2291301	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2291302	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2291303	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2306637	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3754949	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754950	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769859	0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769861	1.00[ASN][1000 genomes]
rs3769862	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3816781	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4894049	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs58152091	1.00[ASN][1000 genomes]
rs60305852	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61680869	1.00[ASN][1000 genomes]
rs719201	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs73973151	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10497524	PLEKHA3	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:179610800-179671400	Weak transcription	Ovary	ovary
4	chr2:179627600-179663800	Weak transcription	Thymus	Thymus
5	chr2:179629600-179666200	Weak transcription	GM12878-XiMat	blood
6	chr2:179632400-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:179639000-179672000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:179639400-179671400	Weak transcription	Gastric	stomach
9	chr2:179646000-179684800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:179647800-179672000	Weak transcription	Fetal Thymus	thymus
11	chr2:179648400-179667200	Weak transcription	HSMM	muscle
12	chr2:179650400-179664400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:179650800-179662800	Weak transcription	Fetal Intestine Large	intestine
14	chr2:179655600-179662400	Genic enhancers	Fetal Heart	heart
15	chr2:179655800-179670800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:179656200-179666200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:179656200-179668400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:179656400-179667600	Weak transcription	Adipose Nuclei	Adipose
19	chr2:179656800-179674400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:179657400-179663800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:179657800-179668800	Weak transcription	Aorta	Aorta
22	chr2:179658200-179666800	Weak transcription	Psoas Muscle	Psoas
23	chr2:179659200-179671400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:179659400-179664800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:179659400-179698000	Weak transcription	Primary B cells from cord blood	blood
26	chr2:179659600-179664800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:179659800-179671200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:179660000-179662400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:179660000-179663800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:179660000-179663800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:179660000-179663800	Weak transcription	Left Ventricle	heart
32	chr2:179660000-179663800	Weak transcription	Pancreas	Pancrea
33	chr2:179660000-179663800	Weak transcription	Right Ventricle	heart
34	chr2:179660000-179669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:179660200-179663600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:179660200-179664000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:179660400-179662400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:179660600-179663600	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:179660600-179663800	Weak transcription	Primary T cells from cord blood	blood
40	chr2:179660600-179663800	Weak transcription	HSMMtube	muscle
41	chr2:179660800-179662200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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