Variant report

Variant	rs2239547
Chromosome Location	chr3:52855229-52855230
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	RAD21	chr3:52854756-52855230	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr3:52854567-52855279	HCT-116	colon:	n/a	n/a
3	CTCF	chr3:52855160-52855310	GM12874	blood:	n/a	n/a
4	CTCF	chr3:52855180-52855330	AoAF	blood vessel:	n/a	n/a
5	CTCF	chr3:52854480-52855269	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr3:52854655-52855229	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr3:52855140-52855290	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52804845..52806455-chr3:52854968..52857676,2	MCF-7	breast:

Variant related genes	Relation type
ITIH4-AS1	TF binding region
ITIH4	TF binding region
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11130331	0.82[JPT][hapmap]
rs11918800	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs11922961	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs11922975	0.82[JPT][hapmap]
rs12488303	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492391	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12496077	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13072536	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083728	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1573815	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2071040	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071041	0.99[ASN][1000 genomes]
rs2071042	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2072391	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240915	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2256332	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2276815	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276817	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276825	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2336668	0.95[JPT][hapmap]
rs2535633	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs35004449	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733047	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3755803	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774364	0.83[ASN][1000 genomes]
rs3821873	0.94[JPT][hapmap]
rs4302374	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4687554	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687559	0.80[ASN][1000 genomes]
rs4687560	0.80[ASN][1000 genomes]
rs4687657	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687663	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687672	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4687680	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4687682	0.95[JPT][hapmap]
rs4687687	0.86[JPT][hapmap]
rs6445538	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6445539	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6445541	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs6445547	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6769789	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6790314	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6795646	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs6797399	0.81[ASN][1000 genomes]
rs6798941	0.86[ASN][1000 genomes]
rs6803519	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs7620706	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7626551	0.86[JPT][hapmap]
rs7638524	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9682464	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9810807	0.95[JPT][hapmap]
rs9836499	0.95[JPT][hapmap]
rs9839035	0.81[ASN][1000 genomes]
rs9844736	0.86[JPT][hapmap]
rs9850563	0.95[JPT][hapmap]
rs9860296	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs9876403	0.91[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap]
rs9880978	0.95[JPT][hapmap]
rs9985365	0.82[JPT][hapmap]

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	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
6	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
7	nsv590308	chr3:52854335-52860806	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Schizophrenia	21926974	GWAS catalog

mRNA abundance (count:24)

SNP	Gene	Cis/trans	Tissue	Source
rs2239547	TMEM110	cis	cerebellum	SCAN
rs2239547	NEK4	cis	parietal	SCAN
rs2239547	GNL3	cis	parietal	SCAN
rs2239547	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2239547	ITIH4	cis	Lymphoblastoid	GTEx
rs2239547	ITIH4-AS1	cis	Whole Blood	GTEx
rs2239547	ITIH4	cis	lymphoblastoid	seeQTL
rs2239547	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2239547	MUSTN1	cis	Artery Aorta	GTEx
rs2239547	ITIH4-AS1	cis	lung	GTEx
rs2239547	ITIH4	cis	parietal	SCAN
rs2239547	ITIH4	cis	multi-tissue	Pritchard
rs2239547	SEMA3G	cis	parietal	SCAN
rs2239547	GLT8D1	cis	lymphoblastoid	seeQTL
rs2239547	GNL3	cis	cerebellum	SCAN
rs2239547	RFT1	cis	cerebellum	SCAN
rs2239547	ITIH4-AS1	cis	Thyroid	GTEx
rs2239547	GLYCTK	cis	parietal	SCAN
rs2239547	WDR6	cis	cerebellum	SCAN
rs2239547	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs2239547	TMEM110	cis	Muscle Skeletal	GTEx
rs2239547	TMEM110	cis	parietal	SCAN
rs2239547	ITIH4	cis	cerebellum	SCAN
rs2239547	RBM6	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52844200-52856600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:52844400-52857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:52844600-52856800	Weak transcription	Fetal Intestine Small	intestine
4	chr3:52844600-52857600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
6	chr3:52846800-52857000	Weak transcription	Aorta	Aorta
7	chr3:52847000-52857400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:52847200-52861200	Genic enhancers	Liver	Liver
9	chr3:52847400-52857000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
11	chr3:52848400-52865800	Weak transcription	Ovary	ovary
12	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
13	chr3:52850600-52857800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
15	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
16	chr3:52851000-52856800	Weak transcription	Fetal Brain Female	brain
17	chr3:52851200-52855400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:52851800-52856800	Weak transcription	Lung	lung
20	chr3:52851800-52858000	Weak transcription	Placenta	Placenta
21	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
23	chr3:52853000-52857000	Weak transcription	Gastric	stomach
24	chr3:52853000-52857000	Enhancers	HepG2	liver
25	chr3:52853000-52857000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr3:52853000-52858400	Strong transcription	Brain Angular Gyrus	brain
27	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:52853200-52855600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr3:52853200-52859400	Strong transcription	Thymus	Thymus
30	chr3:52853400-52856600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:52853400-52857600	Strong transcription	Spleen	Spleen
32	chr3:52853400-52861200	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:52853600-52855600	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:52853800-52855800	Strong transcription	Right Ventricle	heart
35	chr3:52854000-52856600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:52854000-52858800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:52854000-52859000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:52854000-52861200	Strong transcription	Pancreas	Pancrea
39	chr3:52854200-52855600	Strong transcription	Fetal Thymus	thymus
40	chr3:52854200-52859000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:52854400-52856200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:52854400-52856800	Weak transcription	Brain Germinal Matrix	brain
44	chr3:52854400-52861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:52854600-52857400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr3:52855000-52861600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:52855200-52856600	Weak transcription	Brain Anterior Caudate	brain
50	chr3:52855200-52860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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