Variant report

Variant	rs4687552
Chromosome Location	chr3:52838402-52838403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52837977-52840323	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52838396-52838603	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:52836954..52839305-chr3:52853241..52854782,2	K562	blood:
2	chr3:52818249..52820505-chr3:52837668..52840542,3	K562	blood:
3	chr3:52831402..52833454-chr3:52836536..52839409,2	K562	blood:
4	chr3:52831117..52833454-chr3:52835406..52839409,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITIH1-1	chr3:52838019-52838750	NONHSAT089958

No data

Variant related genes	Relation type
ITIH3	TF binding region
ENSG00000055957	Chromatin interaction
ENSG00000055955	Chromatin interaction
ENSG00000162267	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1075653	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1076425	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2019065	0.81[EUR][1000 genomes]
rs2071506	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2071507	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071508	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2239549	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239550	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239551	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239699	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240919	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2240920	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2268023	0.90[ASN][1000 genomes]
rs2270197	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2284350	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2284351	0.81[ASN][1000 genomes]
rs2286798	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2300149	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2535629	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710331	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774354	0.91[ASN][1000 genomes]
rs3774355	0.91[ASN][1000 genomes]
rs4687551	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687654	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6778329	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs678	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs736408	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs746694	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9324	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9881468	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	23974872	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4687552	PBRM1	cis	Thyroid	GTEx
rs4687552	ITIH4-AS1	cis	Artery Aorta	GTEx
rs4687552	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs4687552	MUSTN1	cis	Artery Aorta	GTEx
rs4687552	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs4687552	ITIH4-AS1	cis	Whole Blood	GTEx
rs4687552	ITIH4-AS1	cis	Artery Tibial	GTEx
rs4687552	TMEM110	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52834000-52841600	Strong transcription	HepG2	liver
2	chr3:52834200-52839800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:52835000-52843800	Strong transcription	Liver	Liver
4	chr3:52836800-52851600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:52836800-52851800	Weak transcription	Pancreas	Pancrea
6	chr3:52837200-52839800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:52837200-52841400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:52838000-52847200	Enhancers	Fetal Thymus	thymus
9	chr3:52838200-52840400	Enhancers	Thymus	Thymus
10	chr3:52838400-52852000	Weak transcription	Spleen	Spleen

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