Variant report

Variant	rs6436952
Chromosome Location	chr2:231479012-231479013
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10177471	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10183030	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190300	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10206720	0.86[ASN][1000 genomes]
rs11886067	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902476	0.85[ASN][1000 genomes]
rs12694877	0.89[ASN][1000 genomes]
rs12988735	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13004009	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1305968	0.81[ASN][1000 genomes]
rs1474101	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28612399	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28802613	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28871949	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4343455	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972963	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4972964	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4973338	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436953	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6436955	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6436956	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6436957	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6436958	0.84[ASN][1000 genomes]
rs6436959	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6726627	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748337	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6754758	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7572912	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7575688	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7587015	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6436952	CAB39	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr2:231476200-231479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:231476200-231479400	Weak transcription	Fetal Thymus	thymus
4	chr2:231476200-231479800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:231476200-231479800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:231476200-231479800	Weak transcription	Thymus	Thymus
7	chr2:231476200-231479800	Weak transcription	NH-A	brain
8	chr2:231476200-231479800	Weak transcription	NHEK	skin
9	chr2:231476200-231479800	Weak transcription	Osteobl	bone
10	chr2:231476200-231481000	Weak transcription	Hela-S3	cervix
11	chr2:231476600-231481200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:231476800-231479200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:231476800-231479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:231476800-231481200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:231476800-231482000	Weak transcription	Primary T cells from cord blood	blood
16	chr2:231477000-231479600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:231477000-231480000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:231477200-231480400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:231478600-231479400	Flanking Active TSS	GM12878-XiMat	blood
20	chr2:231478600-231480200	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr2:231478600-231480800	Enhancers	Primary B cells from cord blood	blood
22	chr2:231478600-231481400	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:231479000-231479400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:231479000-231480000	Enhancers	Primary T helper cells fromperipheralblood	blood

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