Variant report

Variant	rs4680589
Chromosome Location	chr3:160198688-160198689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160197463..160200948-chr3:160202172..160205556,5	K562	blood:
2	chr3:160195689..160198943-chr3:160208326..160210743,3	K562	blood:
3	chr3:160191885..160194224-chr3:160197064..160198721,2	MCF-7	breast:
4	chr3:160198112..160200479-chr3:160205569..160207297,2	K562	blood:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1047210	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11706810	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11718121	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12632030	0.83[EUR][1000 genomes]
rs1369666	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1451760	0.84[EUR][1000 genomes]
rs17236473	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17826221	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1971128	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123003	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3732706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3851365	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679654	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679895	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680591	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55992947	0.83[EUR][1000 genomes]
rs56156703	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6785881	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6798183	0.80[EUR][1000 genomes]
rs6798668	0.80[ASN][1000 genomes]
rs6809153	0.81[EUR][1000 genomes]
rs7355951	0.81[EUR][1000 genomes]
rs73875285	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases
8	nsv965125	chr3:160195278-160198798	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4680589	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160190600-160199600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:160193400-160213000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:160195600-160199600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:160195800-160203600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:160196000-160199400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:160196000-160199800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:160196000-160203000	Weak transcription	NHDF-Ad	bronchial
8	chr3:160196200-160203800	Weak transcription	NH-A	brain
9	chr3:160196200-160203800	Weak transcription	NHLF	lung
10	chr3:160196400-160200600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:160196400-160203000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:160196400-160203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:160197200-160198800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:160197200-160199600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:160197800-160203000	Weak transcription	Osteobl	bone
16	chr3:160198600-160199000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:160198600-160199000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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