Variant report

Variant	rs1076425
Chromosome Location	chr3:52825462-52825463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52818572..52822409-chr3:52823256..52828567,5	K562	blood:

Variant related genes	Relation type
ENSG00000055957	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 24 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1014969	0.86[JPT][hapmap]
rs1029871	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1042779	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]
rs10510760	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs1075653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780035	0.94[GIH][hapmap];0.86[JPT][hapmap]
rs10865973	0.86[JPT][hapmap]
rs10865974	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs11130310	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs11130312	0.86[JPT][hapmap]
rs11130315	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs11130317	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs11130323	0.86[JPT][hapmap]
rs11130327	0.83[EUR][1000 genomes]
rs11177	0.94[GIH][hapmap];0.81[JPT][hapmap]
rs11714419	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs11716747	0.86[JPT][hapmap]
rs11717836	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12487591	0.86[JPT][hapmap]
rs12488461	0.94[GIH][hapmap];0.86[JPT][hapmap]
rs12496634	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs12497998	0.86[JPT][hapmap]
rs12635140	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs13061423	0.82[EUR][1000 genomes]
rs13064064	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs13068293	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs13071584	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs13079063	0.90[JPT][hapmap]
rs13082208	0.89[JPT][hapmap]
rs13082960	0.86[JPT][hapmap]
rs13083798	0.81[JPT][hapmap]
rs13085895	0.86[JPT][hapmap]
rs13095332	0.82[EUR][1000 genomes]
rs1561337	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs1866268	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2019065	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2028216	0.94[GIH][hapmap];0.86[JPT][hapmap]
rs2071044	0.83[CHB][hapmap]
rs2071506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071507	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072390	0.86[JPT][hapmap]
rs2079929	0.86[JPT][hapmap]
rs2083180	0.80[GIH][hapmap];0.86[JPT][hapmap]
rs2118540	0.80[JPT][hapmap]
rs2159644	0.86[JPT][hapmap]
rs2164884	0.90[JPT][hapmap]
rs2164885	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs2230534	0.84[EUR][1000 genomes]
rs2230535	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2239549	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239550	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239551	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239699	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240919	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2240920	0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268023	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268024	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2268025	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2268026	0.86[JPT][hapmap]
rs2268027	0.85[JPT][hapmap]
rs2270197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284350	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284351	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286798	0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289247	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2289250	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs2300149	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302417	0.81[ASN][1000 genomes]
rs2336146	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2336149	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs2336545	0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2535629	0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2710323	0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2710331	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33967311	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs34017441	0.91[JPT][hapmap]
rs35526119	0.86[JPT][hapmap]
rs3617	0.82[JPT][hapmap]
rs3733039	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs3733041	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs3733045	0.80[GIH][hapmap];0.86[JPT][hapmap]
rs3755798	0.86[JPT][hapmap]
rs3755806	0.81[GIH][hapmap];0.86[JPT][hapmap]
rs3774354	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774355	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774365	0.86[JPT][hapmap]
rs3774366	0.80[GIH][hapmap];0.86[JPT][hapmap]
rs4481150	0.81[JPT][hapmap]
rs4687548	0.86[JPT][hapmap]
rs4687550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4687551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687552	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687638	0.92[GIH][hapmap];0.86[JPT][hapmap]
rs4687650	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687654	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445534	0.82[JPT][hapmap]
rs6445535	0.86[JPT][hapmap]
rs6617	0.86[JPT][hapmap]
rs6762813	0.94[GIH][hapmap];0.86[JPT][hapmap]
rs6778329	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs678	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792369	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6804145	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs6976	0.94[GIH][hapmap];0.86[JPT][hapmap]
rs736408	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs746694	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7611731	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs7622694	0.82[GIH][hapmap];0.86[JPT][hapmap]
rs7624716	0.86[JPT][hapmap]
rs767418	0.85[JPT][hapmap]
rs8906	0.94[GIH][hapmap];0.86[JPT][hapmap]
rs9324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs998909	0.90[JPT][hapmap];0.81[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

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs1076425	SPCS1	cis	parietal	SCAN
rs1076425	TMEM110	cis	parietal	SCAN
rs1076425	NEK4	cis	cerebellum	SCAN
rs1076425	RBM6	cis	parietal	SCAN
rs1076425	FLJ12442	cis	multi-tissue	Pritchard
rs1076425	TMEM110	cis	cerebellum	SCAN
rs1076425	PBRM1	cis	Thyroid	GTEx
rs1076425	MUSTN1	cis	Artery Aorta	GTEx
rs1076425	WDR6	cis	cerebellum	SCAN
rs1076425	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs1076425	GNL3	cis	parietal	SCAN
rs1076425	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs1076425	RBM6	cis	cerebellum	SCAN
rs1076425	ITIH3	cis	multi-tissue	Pritchard
rs1076425	GNL3	cis	cerebellum	SCAN
rs1076425	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs1076425	ITIH4-AS1	cis	Artery Aorta	GTEx
rs1076425	NEK4	cis	parietal	SCAN
rs1076425	NT5DC2	cis	lymphoblastoid	seeQTL
rs1076425	ITIH4	cis	parietal	SCAN
rs1076425	NT5DC2	cis	multi-tissue	Pritchard
rs1076425	GLT8D1	cis	lymphoblastoid	seeQTL
rs1076425	SEMA3G	cis	parietal	SCAN
rs1076425	ITIH4	cis	lymphoblastoid	seeQTL

Chromatin state (count:8 , 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	chr3:52822600-52826200	Enhancers	HepG2	liver
5	chr3:52823600-52827000	Weak transcription	Spleen	Spleen
6	chr3:52824000-52832800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52825400-52825800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:52825400-52827800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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