Variant report

Variant	rs1520483
Chromosome Location	chr3:46510209-46510210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46508156..46510225-chr3:46511342..46513592,2	K562	blood:
2	chr3:46504252..46506096-chr3:46508837..46511050,2	K562	blood:

Variant related genes	Relation type
ENSG00000012223	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10514713	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10865941	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10865942	0.90[JPT][hapmap]
rs11130093	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs11130094	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap]
rs11706090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489117	0.80[EUR][1000 genomes]
rs12496623	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs12638228	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1402151	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs17030627	1.00[LWK][hapmap]
rs2139634	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683242	0.82[JPT][hapmap]
rs55950019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56233078	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6762703	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6763280	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883739	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs883740	0.82[JPT][hapmap]
rs885485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1520483	LRRC2	cis	brain	seeQTL
rs1520483	KIF9	cis	cerebellum	SCAN
rs1520483	LRRC2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46506800-46510800	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr3:46507400-46522400	Weak transcription	Gastric	stomach
3	chr3:46507600-46514200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:46507800-46513400	Enhancers	Left Ventricle	heart
5	chr3:46508200-46511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:46508200-46511400	Weak transcription	Lung	lung
7	chr3:46508600-46510800	Weak transcription	Pancreas	Pancrea
8	chr3:46509000-46510600	Weak transcription	Adipose Nuclei	Adipose
9	chr3:46509000-46511200	Weak transcription	Spleen	Spleen
10	chr3:46509200-46513400	Enhancers	Psoas Muscle	Psoas
11	chr3:46509400-46514000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:46509600-46511600	Enhancers	Fetal Muscle Leg	muscle
13	chr3:46509600-46511800	Enhancers	Right Atrium	heart
14	chr3:46509600-46512600	Enhancers	Right Ventricle	heart
15	chr3:46509800-46512000	Enhancers	Fetal Muscle Trunk	muscle
16	chr3:46510000-46512400	Enhancers	HSMMtube	muscle
17	chr3:46510200-46511000	Enhancers	Primary B cells from cord blood	blood

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