Variant report

Variant	rs4077787
Chromosome Location	chr4:77003999-77004000
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12510869	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs13130116	0.92[YRI][hapmap]
rs13134119	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13134121	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs17001357	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17001409	0.93[YRI][hapmap]
rs17001416	0.83[YRI][hapmap]
rs4859422	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4859423	0.92[YRI][hapmap]
rs4859425	0.89[YRI][hapmap]
rs4859611	0.91[ASN][1000 genomes]
rs66828967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829592	0.84[YRI][hapmap]
rs6856609	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4077787	NAAA	cis	brain	BrainEAC
rs4077787	NAAA	cis	putamen	BrainEAC
rs4077787	NAAA	cis	Esophagus Mucosa	GTEx
rs4077787	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs4077787	CXCL10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76997000-77007200	Weak transcription	Fetal Brain Male	brain
2	chr4:76997000-77008000	Weak transcription	Brain Angular Gyrus	brain
3	chr4:76999000-77008200	Weak transcription	Right Ventricle	heart
4	chr4:76999400-77004200	Weak transcription	Psoas Muscle	Psoas
5	chr4:76999600-77008000	Weak transcription	Liver	Liver
6	chr4:77001000-77005800	Weak transcription	Fetal Heart	heart
7	chr4:77001000-77006200	Weak transcription	Left Ventricle	heart
8	chr4:77003200-77005000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr4:77003600-77004800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:77003800-77008000	Weak transcription	Brain Anterior Caudate	brain
11	chr4:77003800-77008000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:77003800-77008000	Weak transcription	K562	blood
13	chr4:77003800-77008200	Weak transcription	Fetal Thymus	thymus

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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