Variant report

Variant	rs4504285
Chromosome Location	chr4:80604343-80604344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10033056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11731558	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13116263	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13123790	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13129374	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35385700	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35780399	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35937876	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3924925	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4292357	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4470656	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55789335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57395415	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6534482	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67659266	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6813424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821475	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7683198	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879506	chr4:80316417-80604625	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1002031	chr4:80459528-80759113	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1005152	chr4:80549659-80814456	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv997478	chr4:80578536-80669871	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1006225	chr4:80578536-80670045	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv521454	chr4:80598796-80654020	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv594737	chr4:80598796-80669947	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4504285	CCNG2	cis	cerebellum	SCAN
rs4504285	MRPL1	cis	cerebellum	SCAN
rs4504285	CXCL13	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:80601200-80606000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:80601600-80605800	Weak transcription	Dnd41	blood
3	chr4:80602800-80604600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:80603200-80604400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:80603200-80604400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:80603200-80604400	Enhancers	NH-A	brain
7	chr4:80603400-80604400	Enhancers	Brain Germinal Matrix	brain
8	chr4:80603400-80604600	Enhancers	Colon Smooth Muscle	Colon
9	chr4:80603800-80604600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr4:80604000-80604400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr4:80604000-80604400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:80604000-80604400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:80604000-80604400	Enhancers	Aorta	Aorta
14	chr4:80604000-80604400	Enhancers	Brain Anterior Caudate	brain
15	chr4:80604000-80604400	Enhancers	Brain Substantia Nigra	brain
16	chr4:80604000-80604400	Enhancers	Fetal Muscle Trunk	muscle
17	chr4:80604000-80604400	Enhancers	Fetal Muscle Leg	muscle
18	chr4:80604000-80604400	Enhancers	Gastric	stomach
19	chr4:80604000-80604400	Enhancers	Psoas Muscle	Psoas
20	chr4:80604000-80604600	Enhancers	Fetal Brain Male	brain
21	chr4:80604000-80604600	Enhancers	Fetal Brain Female	brain
22	chr4:80604000-80604600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr4:80604200-80604400	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr4:80604200-80604400	Enhancers	Brain Hippocampus Middle	brain
25	chr4:80604200-80604400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr4:80604200-80604600	Enhancers	Stomach Smooth Muscle	stomach

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