Variant report

Variant	rs6831523
Chromosome Location	chr4:20742554-20742555
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10516361	0.92[ASN][1000 genomes]
rs1061836	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1080125	0.81[ASN][1000 genomes]
rs11721944	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723855	0.96[ASN][1000 genomes]
rs11733451	0.81[ASN][1000 genomes]
rs11736309	0.81[ASN][1000 genomes]
rs11736477	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737893	0.85[ASN][1000 genomes]
rs12498799	0.81[ASN][1000 genomes]
rs12503714	0.92[ASN][1000 genomes]
rs12509329	0.94[ASN][1000 genomes]
rs12510666	0.87[ASN][1000 genomes]
rs1365580	0.89[ASN][1000 genomes]
rs1365581	0.89[ASN][1000 genomes]
rs1426882	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16869859	0.92[ASN][1000 genomes]
rs16869884	0.92[ASN][1000 genomes]
rs17552950	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17622121	0.85[ASN][1000 genomes]
rs2291530	0.96[ASN][1000 genomes]
rs28439580	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2874831	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56267013	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs57364495	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59020971	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62410066	0.85[ASN][1000 genomes]
rs62410087	0.85[ASN][1000 genomes]
rs62410132	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62410133	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62410158	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411661	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73101456	0.85[ASN][1000 genomes]
rs964020	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869522	chr4:20724433-20938248	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6831523	C4orf28	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20725000-20753000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:20730600-20757600	Weak transcription	HSMM	muscle
3	chr4:20732600-20758400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:20736000-20747800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:20739200-20748200	Weak transcription	Psoas Muscle	Psoas
6	chr4:20739200-20761200	Weak transcription	Fetal Heart	heart
7	chr4:20739600-20755200	Weak transcription	K562	blood
8	chr4:20740200-20755200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:20740600-20742800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:20740600-20743400	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:20740600-20754800	Weak transcription	Dnd41	blood
12	chr4:20740600-20756600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:20740600-20757200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:20740600-20763600	Weak transcription	Brain Anterior Caudate	brain
15	chr4:20740800-20742800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:20740800-20746400	Weak transcription	Left Ventricle	heart
17	chr4:20740800-20750800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:20740800-20751400	Weak transcription	Pancreas	Pancrea
19	chr4:20740800-20756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:20740800-20757200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:20740800-20757600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr4:20740800-20763600	Weak transcription	HSMMtube	muscle
23	chr4:20740800-20770600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:20740800-20791200	Weak transcription	Ovary	ovary
25	chr4:20741000-20749200	Weak transcription	Fetal Stomach	stomach
26	chr4:20741000-20753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:20741000-20757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:20741600-20754200	Weak transcription	Fetal Lung	lung
29	chr4:20741600-20756200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:20741800-20757400	Weak transcription	Primary T cells from cord blood	blood

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