Variant report

Variant	rs4687663
Chromosome Location	chr3:52870618-52870619
allele	A/T
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	EBF1	chr3:52870460-52870824	GM12878	blood:	n/a	chr3:52870648-52870659
2	EBF1	chr3:52870458-52870877	GM12878	blood:	n/a	chr3:52870648-52870659
3	EBF1	chr3:52870420-52870803	GM12878	blood:	n/a	chr3:52870648-52870659

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52865265..52868196-chr3:52870244..52872785,3	K562	blood:
2	chr3:52866935..52869268-chr3:52870360..52872444,2	K562	blood:

Variant related genes	Relation type
MUSTN1	TF binding region
ENSG00000243696	TF binding region
ENSG00000055955	Chromatin interaction
ENSG00000243696	Chromatin interaction
ENSG00000272573	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1134546	0.82[CEU][hapmap]
rs11918800	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs11922961	0.83[CHB][hapmap]
rs12488303	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12492391	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs12496077	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001735	0.85[ASN][1000 genomes]
rs2071040	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071041	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071042	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2072391	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239547	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]
rs2240915	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs2256332	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2276815	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2276817	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276825	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336666	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2336668	0.91[JPT][hapmap]
rs2336669	0.82[CEU][hapmap]
rs2535633	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2564947	0.82[CEU][hapmap]
rs2581801	0.81[CEU][hapmap]
rs2581815	0.82[CEU][hapmap]
rs2878762	0.84[ASN][1000 genomes]
rs35004449	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3733047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755803	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821873	0.94[JPT][hapmap]
rs4302374	0.82[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4519686	0.82[CEU][hapmap]
rs4687554	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687559	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4687560	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4687657	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687658	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687680	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs4687682	0.91[JPT][hapmap]
rs4687687	0.81[JPT][hapmap]
rs6445538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445541	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6445547	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6445550	0.82[CEU][hapmap]
rs6768844	0.82[CEU][hapmap]
rs6769789	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6790314	0.89[YRI][hapmap]
rs6792578	0.82[CEU][hapmap]
rs6795646	0.90[JPT][hapmap]
rs6797399	0.86[ASN][1000 genomes]
rs6798941	0.92[ASN][1000 genomes]
rs6803519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7620706	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626551	0.81[JPT][hapmap]
rs7638524	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9311485	0.82[CEU][hapmap]
rs9682464	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810807	0.90[JPT][hapmap]
rs9836499	0.90[JPT][hapmap]
rs9839035	0.86[ASN][1000 genomes]
rs9844736	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs9846976	0.82[CEU][hapmap]
rs9850563	0.91[JPT][hapmap]
rs9860296	0.90[JPT][hapmap]
rs9865094	0.81[CEU][hapmap]
rs9876403	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9880978	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4687663	ITIH4-AS1	cis	lung	GTEx
rs4687663	ITIH4	cis	Lymphoblastoid	GTEx
rs4687663	TMEM110	cis	Muscle Skeletal	GTEx
rs4687663	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs4687663	MUSTN1	cis	Artery Aorta	GTEx
rs4687663	ITIH4	cis	multi-tissue	Pritchard
rs4687663	ITIH4-AS1	cis	Whole Blood	GTEx
rs4687663	ITIH4-AS1	cis	Artery Aorta	GTEx
rs4687663	ITIH4-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:52865600-52875200	Weak transcription	Dnd41	blood
9	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
10	chr3:52866000-52884800	Weak transcription	HMEC	breast
11	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
13	chr3:52866200-52885200	Weak transcription	NHEK	skin
14	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
15	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
17	chr3:52866600-52879200	Weak transcription	Osteobl	bone
18	chr3:52866800-52871000	Strong transcription	Spleen	Spleen
19	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
22	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
23	chr3:52867000-52871000	Strong transcription	Thymus	Thymus
24	chr3:52867000-52871200	Weak transcription	Pancreas	Pancrea
25	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:52867200-52871400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:52867600-52871800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:52867800-52871200	Enhancers	Right Ventricle	heart
32	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:52868400-52871400	Enhancers	Fetal Heart	heart
35	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
36	chr3:52868600-52872000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:52868800-52873000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:52869000-52873400	Strong transcription	Brain Anterior Caudate	brain
41	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
43	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
44	chr3:52869200-52871200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:52869200-52871600	Enhancers	Right Atrium	heart
46	chr3:52869200-52871800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:52869200-52871800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr3:52869200-52873000	Strong transcription	Primary B cells from cord blood	blood
49	chr3:52869400-52871200	Enhancers	Left Ventricle	heart
50	chr3:52869400-52872800	Weak transcription	Rectal Mucosa Donor 29	rectum

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