Variant report

Variant	rs2622765
Chromosome Location	chr15:52040076-52040077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:52039828-52040097	HepG2	liver:	n/a	chr15:52039944-52039955
2	CEBPB	chr15:52039818-52040105	K562	blood:	n/a	chr15:52039944-52039955
3	CEBPB	chr15:52039879-52040100	A549	lung:	n/a	chr15:52039944-52039955

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52028203..52034388-chr15:52036095..52042039,7	K562	blood:
2	chr15:52032888..52035475-chr15:52037626..52040413,3	K562	blood:

Variant related genes	Relation type
ENSG00000259377	TF binding region
TMOD2	TF binding region
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1133878	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964482	1.00[CHB][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs16964483	1.00[CHB][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs17611465	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1972419	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1991267	1.00[CHB][hapmap]
rs2016057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124587	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448810	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2554354	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554355	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2554358	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570243	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2593169	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2593181	1.00[CHB][hapmap]
rs2606128	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2606130	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606133	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2606147	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622778	1.00[CHB][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs2623245	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623247	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623251	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623263	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2623270	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2652595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652597	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28522862	1.00[ASN][1000 genomes]
rs28654101	1.00[ASN][1000 genomes]
rs28876142	1.00[ASN][1000 genomes]
rs691738	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71472920	1.00[ASN][1000 genomes]

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	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2622765	SCG3	cis	Frontal Cortex	GTEx
rs2622765	SCG3	cis	Cerebellum	GTEx
rs2622765	SCG3	cis	Temporal Cortex	GTEx
rs2622765	SCG3	cis	Brain Pons	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52030600-52043200	Weak transcription	Gastric	stomach
2	chr15:52031200-52043000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52032400-52040800	Weak transcription	K562	blood

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