Variant report

Variant	rs4823074
Chromosome Location	chr22:30512478-30512479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30510772..30513351-chr22:30653868..30656059,2	MCF-7	breast:
2	chr22:30510449..30512616-chr22:30646974..30649520,2	MCF-7	breast:
3	chr22:30510247..30512648-chr22:30515643..30517309,2	K562	blood:
4	chr22:30507793..30510712-chr22:30511298..30514202,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1003342	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs193477	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1989870	0.81[JPT][hapmap]
rs2412970	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412971	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412975	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41173	0.81[JPT][hapmap]
rs4823073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4823075	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4823077	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5763767	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997579	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6006356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs713875	0.92[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs714027	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757024	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv588884	chr22:30494371-30590026	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4823074	TTC28	cis	cerebellum	SCAN
rs4823074	CABP7	cis	cerebellum	SCAN
rs4823074	MTMR3	cis	parietal	SCAN
rs4823074	ASCC2	cis	cerebellum	SCAN
rs4823074	NEFH	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30510600-30513000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr22:30511200-30513600	Enhancers	Fetal Intestine Small	intestine
3	chr22:30511200-30514400	Enhancers	Fetal Intestine Large	intestine
4	chr22:30511600-30513200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:30511800-30512600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr22:30511800-30512800	Enhancers	NHDF-Ad	bronchial
7	chr22:30511800-30513000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:30511800-30513000	Enhancers	NH-A	brain
9	chr22:30511800-30513000	Enhancers	NHLF	lung
10	chr22:30511800-30513200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr22:30511800-30513200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr22:30511800-30513200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr22:30511800-30513200	Enhancers	Osteobl	bone
14	chr22:30511800-30513400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr22:30511800-30513400	Enhancers	HMEC	breast
16	chr22:30511800-30513400	Enhancers	HSMM	muscle
17	chr22:30511800-30513400	Enhancers	HSMMtube	muscle
18	chr22:30512000-30512600	Enhancers	Fetal Lung	lung
19	chr22:30512000-30513400	Enhancers	NHEK	skin
20	chr22:30512200-30512600	Flanking Active TSS	A549	lung
21	chr22:30512200-30513000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:30512200-30513000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:30512200-30513200	Enhancers	Hela-S3	cervix
24	chr22:30512200-30513200	Enhancers	HepG2	liver
25	chr22:30512400-30513000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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