Variant report

Variant	rs2577424
Chromosome Location	chr5:128312492-128312493
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	chr5:128309200..128312027-chr5:128312366..128314966,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11740215	0.84[CEU][hapmap]
rs13190393	0.81[CEU][hapmap]
rs1496347	0.85[CEU][hapmap]
rs17616974	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs17616991	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs1833549	0.84[CEU][hapmap]
rs2522383	0.96[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs2526243	0.80[CEU][hapmap]
rs2526246	0.84[YRI][hapmap]
rs2526248	0.84[CEU][hapmap]
rs2526249	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2526251	0.84[CEU][hapmap]
rs2526255	0.96[CEU][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526257	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2545015	0.80[CEU][hapmap]
rs2545024	0.81[JPT][hapmap]
rs2577429	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2577436	0.83[CEU][hapmap]
rs2577489	0.96[CEU][hapmap];0.81[JPT][hapmap]
rs2577535	0.80[YRI][hapmap]
rs2577542	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2577543	0.83[CEU][hapmap]
rs2577545	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs2577546	0.84[CEU][hapmap]
rs257894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs257902	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs257998	0.81[CHB][hapmap]
rs6859755	0.88[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs7702784	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882839	chr5:128205828-128390167	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv882840	chr5:128205828-128428962	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830485	chr5:128298622-128480492	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv882841	chr5:128301971-128400356	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv882842	chr5:128301971-128552706	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2577424	SHROOM1	cis	cerebellum	SCAN
rs2577424	SLC27A6	cis	Nerve Tibial	GTEx
rs2577424	SLC27A6	cis	parietal	SCAN
rs2577424	SLC27A6	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128303200-128312600	Weak transcription	Fetal Heart	heart
2	chr5:128303400-128319400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:128309600-128338200	Weak transcription	Left Ventricle	heart
4	chr5:128311800-128312800	Weak transcription	Brain Cingulate Gyrus	brain

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