Variant report

Variant	rs4343455
Chromosome Location	chr2:231481198-231481199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10177471	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183030	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10190300	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10206720	0.87[ASN][1000 genomes]
rs11886067	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902476	0.85[ASN][1000 genomes]
rs12694877	0.89[ASN][1000 genomes]
rs12988735	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004009	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1305968	0.80[ASN][1000 genomes]
rs1474101	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28612399	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28802613	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28871949	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972963	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4972964	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4973338	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6436952	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436953	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436955	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436956	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436957	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436958	0.84[ASN][1000 genomes]
rs6436959	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726627	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748337	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6754758	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7572912	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7575688	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7587015	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[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	nsv875955	chr2:231440555-231500805	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4343455	IRS1	cis	parietal	SCAN
rs4343455	CAB39	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231472800-231497200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:231476600-231481200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:231476800-231481200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:231476800-231482000	Weak transcription	Primary T cells from cord blood	blood
5	chr2:231478600-231481400	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:231479200-231481800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:231479200-231482000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:231479800-231481800	Enhancers	HMEC	breast
9	chr2:231479800-231482000	Enhancers	NH-A	brain
10	chr2:231479800-231482000	Enhancers	NHDF-Ad	bronchial
11	chr2:231479800-231482600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr2:231479800-231482600	Enhancers	HSMM	muscle
13	chr2:231479800-231482600	Enhancers	NHEK	skin
14	chr2:231479800-231482800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:231480000-231481200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:231480000-231481200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:231480000-231482600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:231480200-231481200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:231480200-231481200	Weak transcription	Fetal Thymus	thymus
20	chr2:231480200-231481200	Weak transcription	A549	lung
21	chr2:231480200-231481200	Weak transcription	Osteobl	bone
22	chr2:231480400-231481600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:231480400-231481800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:231480600-231481600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:231480600-231482000	Enhancers	GM12878-XiMat	blood
26	chr2:231480800-231481600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:231481000-231481400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:231481000-231481400	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr2:231481000-231482200	Enhancers	NHLF	lung
30	chr2:231481000-231482800	Enhancers	Hela-S3	cervix

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