Variant report

Variant	rs2710323
Chromosome Location	chr3:52815905-52815906
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	FOXA2	chr3:52815770-52816026	HepG2	liver:	n/a	n/a
2	FOXA1	chr3:52815720-52815963	T-47D	breast:	n/a	n/a
3	FOXA1	chr3:52815652-52815976	HepG2	liver:	n/a	n/a
4	FOXA1	chr3:52815748-52815987	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52810201..52813170-chr3:52814062..52816264,2	K562	blood:

Variant related genes	Relation type
ITIH1	TF binding region
ENSG00000055957	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1014969	0.83[GIH][hapmap]
rs1042779	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1075653	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1076425	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1108842	0.85[CEU][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs11130324	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11716747	0.88[GIH][hapmap]
rs12487445	0.81[JPT][hapmap]
rs12497998	0.88[GIH][hapmap]
rs13071584	0.88[GIH][hapmap]
rs13079063	0.88[GIH][hapmap];0.81[JPT][hapmap]
rs13082208	0.80[CHB][hapmap]
rs13082960	0.90[GIH][hapmap]
rs13083798	0.84[CEU][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs2019065	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2071044	0.84[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs2071506	0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2071507	0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2071508	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2072390	0.88[GIH][hapmap]
rs2079929	0.88[GIH][hapmap]
rs2159644	0.88[GIH][hapmap]
rs2164884	0.81[JPT][hapmap]
rs2164885	0.81[JPT][hapmap]
rs2230535	0.91[GIH][hapmap]
rs2239549	0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239550	0.86[ASN][1000 genomes]
rs2239551	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2239699	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2240919	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2240920	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2268023	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2268025	0.82[CHB][hapmap]
rs2268026	0.91[GIH][hapmap]
rs2270197	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2276824	0.86[JPT][hapmap]
rs2284351	0.80[ASN][1000 genomes]
rs2286798	0.87[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2300149	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2302417	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2336545	0.91[GIH][hapmap]
rs2535627	0.84[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2535629	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[ASN][1000 genomes]
rs2577831	0.91[ASW][hapmap];0.88[CEU][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs2590838	0.82[ASW][hapmap];0.84[CEU][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap]
rs34017441	0.91[GIH][hapmap];0.82[JPT][hapmap]
rs35526119	0.88[GIH][hapmap]
rs3617	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3755798	0.88[GIH][hapmap]
rs3774354	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3774355	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4481150	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687550	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4687551	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4687654	0.86[ASN][1000 genomes]
rs6445535	0.88[GIH][hapmap]
rs6778329	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs678	0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs6792369	0.88[ASN][1000 genomes]
rs736408	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs746694	0.81[ASN][1000 genomes]
rs7624716	0.88[GIH][hapmap]
rs7646741	0.84[EUR][1000 genomes]
rs767418	0.88[GIH][hapmap]
rs9324	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs9879090	0.86[JPT][hapmap]
rs9881468	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs998909	0.81[JPT][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	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

Variant related diseases (count:2)

Disease	PMID	Source
Glaucoma (primary open-angle)	25173105	GWAS catalog
Schizophrenia, schizoaffective disorder or bipolar disorder	24166486	GWAS catalog

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs2710323	SEMA3G	cis	parietal	SCAN
rs2710323	PBRM1	cis	Thyroid	GTEx
rs2710323	WDR6	cis	cerebellum	SCAN
rs2710323	GNL3	cis	cerebellum	SCAN
rs2710323	ITIH4	cis	Lymphoblastoid	GTEx
rs2710323	NEK4	cis	cerebellum	SCAN
rs2710323	GLYCTK	cis	parietal	SCAN
rs2710323	RBM6	cis	cerebellum	SCAN
rs2710323	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs2710323	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2710323	FLJ12442	cis	multi-tissue	Pritchard
rs2710323	NEK4	cis	parietal	SCAN
rs2710323	GLT8D1	cis	lymphoblastoid	seeQTL
rs2710323	GNL3	cis	parietal	SCAN
rs2710323	NT5DC2	cis	lymphoblastoid	seeQTL
rs2710323	SPCS1	cis	parietal	SCAN
rs2710323	ITFG2	trans	cerebellum	SCAN
rs2710323	NT5DC2	cis	multi-tissue	Pritchard
rs2710323	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs2710323	ITIH4	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52805600-52825800	Weak transcription	Right Ventricle	heart
2	chr3:52810200-52816600	Enhancers	HepG2	liver
3	chr3:52812000-52816200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr3:52814800-52826400	Genic enhancers	Liver	Liver
5	chr3:52815600-52816200	Enhancers	Fetal Thymus	thymus
6	chr3:52815800-52816200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:52815800-52816200	Active TSS	Spleen	Spleen
8	chr3:52815800-52816400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52815800-52816600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell

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