Variant report

Variant	rs736408
Chromosome Location	chr3:52835354-52835355
allele	A/G
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	POLR2A	chr3:52835268-52835500	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52817973..52820437-chr3:52833631..52835650,3	K562	blood:
2	chr3:52827519..52829330-chr3:52834424..52837850,3	MCF-7	breast:
3	chr3:52834279..52837211-chr3:52858122..52860407,2	K562	blood:

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

Extended variants
information (count: 52 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1042779	0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1075653	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1076425	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13079063	0.81[JPT][hapmap]
rs13082208	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2019065	0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2071044	0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2071506	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2071507	0.83[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2071508	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164885	0.81[JPT][hapmap]
rs2239549	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239550	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239551	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239699	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2240919	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs2240920	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2268023	0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2268025	0.82[CHB][hapmap]
rs2270197	0.81[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2284350	0.81[EUR][1000 genomes]
rs2286798	0.87[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2300149	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2535627	0.87[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2535629	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2710323	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2710331	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34017441	0.82[JPT][hapmap]
rs3617	0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3774354	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3774355	0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4481150	0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4687550	0.83[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs4687551	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687552	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687654	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6769789	0.83[YRI][hapmap]
rs6778329	0.87[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs678	0.88[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6792369	0.86[ASN][1000 genomes]
rs746694	0.86[EUR][1000 genomes]
rs9324	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9881468	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998909	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv3452194	chr3:52832512-52836010	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder	21926972	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs736408	FLJ12442	cis	multi-tissue	Pritchard
rs736408	PBRM1	cis	Thyroid	GTEx
rs736408	ITIH4	cis	multi-tissue	Pritchard
rs736408	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs736408	ITIH4-AS1	cis	Artery Aorta	GTEx
rs736408	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs736408	ITIH4	cis	Lymphoblastoid	GTEx
rs736408	ITIH4-AS1	cis	Artery Tibial	GTEx
rs736408	MUSTN1	cis	Artery Aorta	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:52828200-52835800	Weak transcription	HSMMtube	muscle
3	chr3:52830400-52836400	Weak transcription	Pancreas	Pancrea
4	chr3:52833000-52836200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:52833000-52836400	Weak transcription	HSMM	muscle
6	chr3:52833200-52835600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:52833600-52835800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:52834000-52838000	Weak transcription	Fetal Thymus	thymus
9	chr3:52834000-52841600	Strong transcription	HepG2	liver
10	chr3:52834200-52839800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:52834600-52836400	Weak transcription	Spleen	Spleen
12	chr3:52834800-52835800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:52834800-52836200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:52835000-52843800	Strong transcription	Liver	Liver

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