Variant report

Variant	rs1077834
Chromosome Location	chr15:58723479-58723480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1077835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800588	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261332	0.86[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs261334	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs261342	0.86[CEU][hapmap]
rs588136	0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs8033940	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2760372	chr15:58721447-58731153	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hematological and biochemical traits	20139978	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1077834	FAM63B	cis	cerebellum	SCAN
rs1077834	LIPC	cis	multi-tissue	Pritchard
rs1077834	RFX7	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58704600-58728800	Weak transcription	Thymus	Thymus
2	chr15:58716600-58725800	Weak transcription	Right Atrium	heart
3	chr15:58716600-58726600	Weak transcription	Esophagus	oesophagus
4	chr15:58717800-58723600	Weak transcription	Pancreas	Pancrea
5	chr15:58717800-58724400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:58718000-58724600	Weak transcription	NHDF-Ad	bronchial
7	chr15:58718200-58723600	Weak transcription	Fetal Intestine Large	intestine
8	chr15:58718400-58726600	Weak transcription	Stomach Mucosa	stomach
9	chr15:58718600-58725000	Weak transcription	Fetal Lung	lung
10	chr15:58719600-58725800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:58722000-58723800	Flanking Active TSS	Liver	Liver
12	chr15:58722000-58724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:58722400-58723600	Weak transcription	Fetal Thymus	thymus
14	chr15:58722600-58723800	Enhancers	K562	blood
15	chr15:58722600-58724200	Weak transcription	Right Ventricle	heart
16	chr15:58722600-58731000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:58723400-58724000	Flanking Active TSS	HepG2	liver
18	chr15:58723400-58724200	Enhancers	A549	lung
19	chr15:58723400-58724400	Enhancers	Fetal Kidney	kidney

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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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