Variant report

Variant	rs1042779
Chromosome Location	chr3:52821011-52821012
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	chr3:52820970-52821091	HepG2	liver:	n/a	n/a
2	NR2F2	chr3:52820201-52821296	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52820991-52821087	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52819022..52821940-chr3:52830532..52832899,2	K562	blood:
2	chr3:52818572..52822409-chr3:52823256..52828567,5	K562	blood:
3	chr3:52804965..52807932-chr3:52819198..52822291,3	K562	blood:

Variant related genes	Relation type
ITIH1	TF binding region
ENSG00000114904	Chromatin interaction
ENSG00000055957	Chromatin interaction
ENSG00000162267	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1014969	0.83[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1029871	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs10510760	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1075653	1.00[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1076425	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10780035	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs10865973	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10865974	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs1108842	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11130310	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs11130312	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11130315	0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs11130317	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs11130323	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11130327	0.84[EUR][1000 genomes]
rs11177	0.83[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs11714419	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs11716747	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs11717836	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12487591	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs12488461	0.86[JPT][hapmap]
rs12496634	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs12497998	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs12635140	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs13061423	0.85[EUR][1000 genomes]
rs13064064	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs13068293	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs13071584	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13079063	0.82[CHB][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs13082208	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs13082960	0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs13083798	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs13085775	0.82[MKK][hapmap]
rs13085895	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs13095332	0.83[EUR][1000 genomes]
rs1561337	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs1866268	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs2019065	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2028216	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs2071044	0.87[CHB][hapmap]
rs2071506	1.00[ASW][hapmap];0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071507	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2071508	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072390	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2079929	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs2083180	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap]
rs2098167	0.84[ASN][1000 genomes]
rs2118540	0.81[JPT][hapmap]
rs2159644	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs2164884	0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs2164885	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2230534	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2230535	0.83[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2239549	0.86[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239551	0.82[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239699	0.90[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2240919	0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2240920	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2268023	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2268024	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2268025	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2268026	0.83[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2268027	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2270197	0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276824	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2284350	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2284351	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286798	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289247	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs2289250	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2300149	0.86[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2302417	0.90[ASN][1000 genomes]
rs2336146	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs2336149	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs2336545	0.83[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2535627	0.83[CHB][hapmap]
rs2535629	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577831	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2590838	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs2710323	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs33967311	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs34017441	0.83[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap]
rs35526119	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs3617	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3733039	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs3733041	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs3733045	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs3755798	0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs3755799	0.83[CHD][hapmap]
rs3755806	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs3774354	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774355	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774365	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs3774366	0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs3852066	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs4481150	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4687548	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4687550	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4687551	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687638	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs4687650	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4687654	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62255396	0.80[EUR][1000 genomes]
rs6445534	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs6445535	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs6617	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6762813	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs6778329	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792369	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804145	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs6976	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs736408	0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs746694	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611731	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs7622694	0.83[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs7624716	0.83[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs767418	0.83[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap]
rs8906	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs9324	0.89[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.91[JPT][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9879090	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs9881468	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs998909	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][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
Bipolar disorder	19416921	GWAS catalog

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1042779	FLJ12442	cis	multi-tissue	Pritchard
rs1042779	GNL3	cis	cerebellum	SCAN
rs1042779	ITIH4-AS1	cis	Artery Aorta	GTEx
rs1042779	NT5DC2	cis	multi-tissue	Pritchard
rs1042779	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs1042779	NEK4	cis	parietal	SCAN
rs1042779	NEK4	cis	cerebellum	SCAN
rs1042779	GNL3	cis	parietal	SCAN
rs1042779	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs1042779	PBRM1	cis	Thyroid	GTEx
rs1042779	NT5DC2	cis	lymphoblastoid	seeQTL
rs1042779	GLYCTK	cis	parietal	SCAN
rs1042779	ITIH4	cis	parietal	SCAN
rs1042779	ITIH4	cis	multi-tissue	Pritchard
rs1042779	TMEM110	cis	parietal	SCAN
rs1042779	MUSTN1	cis	Artery Aorta	GTEx
rs1042779	SPCS1	cis	parietal	SCAN
rs1042779	GLT8D1	cis	lymphoblastoid	seeQTL
rs1042779	TMEM110	cis	cerebellum	SCAN
rs1042779	RBM6	cis	cerebellum	SCAN
rs1042779	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs1042779	RBM6	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52805600-52825800	Weak transcription	Right Ventricle	heart
2	chr3:52814800-52826400	Genic enhancers	Liver	Liver
3	chr3:52816400-52825800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:52819600-52823000	Weak transcription	Spleen	Spleen
5	chr3:52820400-52822600	Flanking Active TSS	HepG2	liver

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