Variant report

Variant	rs2276823
Chromosome Location	chr3:52869263-52869264
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZBTB7A	chr3:52869119-52869290	HepG2	liver:	n/a	n/a
2	TEAD4	chr3:52869087-52869523	H1-hESC	embryonic stem cell:	n/a	chr3:52869319-52869328
3	TEAD4	chr3:52869116-52869495	HepG2	liver:	n/a	chr3:52869319-52869328

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52869263-52869313	U87	brain:	n/a
2	chr3:52869263-52869313	MCF-7	breast:	n/a
3	chr3:52869263-52869313	ProgFib	skin:	n/a
4	chr3:52869263-52869313	HNPCEpiC	eye:	n/a
5	chr3:52869263-52869313	CMK	blood:	n/a
6	chr3:52869263-52869313	Caco-2	colon:	n/a
7	chr3:52869263-52869313	GM12891	blood:	n/a
8	chr3:52869263-52869313	ECC-1	luminal epithelium:	n/a
9	chr3:52869263-52869313	K562	blood:	n/a
10	chr3:52869263-52869313	Jurkat	blood:	n/a
11	chr3:52869263-52869313	NH-A	brain:	n/a
12	chr3:52869263-52869313	HCM	heart:	n/a
13	chr3:52869263-52869313	HRE	kidney:	n/a
14	chr3:52869263-52869313	AG04449	skin:	fetal
15	chr3:52869263-52869313	HMEC	breast:	n/a
16	chr3:52869263-52869313	SAEC	small airway:	n/a
17	chr3:52869263-52869313	NB4	blood:	n/a
18	chr3:52869263-52869313	GM19239	blood:	n/a
19	chr3:52869263-52869313	IMR90	lung:	fetal
20	chr3:52869263-52869313	HepG2	liver:	n/a
21	chr3:52869263-52869313	GM12878	blood:	n/a
22	chr3:52869263-52869313	PFSK-1	brain:	n/a
23	chr3:52869263-52869313	AG09319	gingival:	n/a
24	chr3:52869263-52869313	HRPEpiC	eye:	n/a
25	chr3:52869263-52869313	SK-N-MC	brain:	n/a
26	chr3:52869263-52869313	SKMC	muscle:	n/a
27	chr3:52869263-52869313	RPTEC	kidney:	n/a
28	chr3:52869263-52869313	HL-60	blood:	n/a
29	chr3:52869263-52869313	AoSMC	blood vessel:	n/a
30	chr3:52869263-52869313	T-47D	breast:	n/a
31	chr3:52869263-52869313	SK-N-SH_RA	brain:	n/a
32	chr3:52869263-52869313	HCF	heart:	n/a
33	chr3:52869263-52869313	NHDF-neo	bronchial:	n/a
34	chr3:52869263-52869313	HRCEpiC	kidney:	n/a
35	chr3:52869263-52869313	Hepatocyte	liver:	n/a
36	chr3:52869263-52869313	MCF10A-Er-Src	breast:	n/a
37	chr3:52869263-52869313	HUVEC	blood vessel:	n/a
38	chr3:52869263-52869313	HAEpiC	amniotic membrane:	n/a
39	chr3:52869263-52869313	PANC-1	pancreas:	n/a
40	chr3:52869263-52869313	LNCaP	prostate:	n/a
41	chr3:52869263-52869313	HEEpiC	esophagus:	n/a
42	chr3:52869263-52869313	BE2_C	brain:	n/a
43	chr3:52869263-52869313	AG04450	lung:	fetal
44	chr3:52869263-52869313	PrEC	prostate:	n/a
45	chr3:52869263-52869313	HIPEpiC	eye:	n/a
46	chr3:52869263-52869313	A549	lung:	n/a
47	chr3:52869263-52869313	NT2-D1	testis:	n/a
48	chr3:52869263-52869313	ovcar-3	ovarian:	n/a
49	chr3:52869263-52869313	AG09309	skin:	n/a
50	chr3:52869263-52869313	BJ	skin:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52867798..52869834-chr3:52876401..52878497,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243696	TF binding region
ITIH4	TF binding region
MUSTN1	TF binding region
ITIH4	CpG island
MUSTN1	CpG island
ENSG00000243696	CpG island
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10865977	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11715347	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11915546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11918800	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922961	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487379	0.87[EUR][1000 genomes]
rs13072537	0.86[EUR][1000 genomes]
rs2239548	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2240915	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2240917	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2245538	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2245647	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2256332	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2336558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336664	0.80[ASN][1000 genomes]
rs2535633	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3774364	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4350911	0.81[EUR][1000 genomes]
rs4687682	0.83[AMR][1000 genomes]
rs56019197	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56383738	0.80[ASN][1000 genomes]
rs60332615	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445541	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6764322	0.81[EUR][1000 genomes]
rs6769789	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773650	0.81[EUR][1000 genomes]
rs7612624	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7617468	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7620690	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7630552	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7652667	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9836499	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9850563	0.82[AMR][1000 genomes]
rs9866243	0.81[AMR][1000 genomes]
rs9880978	0.81[AMR][1000 genomes]

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	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	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
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2276823	ITIH4-AS1	cis	Artery Tibial	GTEx
rs2276823	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2276823	ITIH4-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 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	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:52865600-52875200	Weak transcription	Dnd41	blood
10	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
11	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:52866000-52884800	Weak transcription	HMEC	breast
13	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:52866200-52870200	Weak transcription	Gastric	stomach
15	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
17	chr3:52866200-52885200	Weak transcription	NHEK	skin
18	chr3:52866400-52869800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
20	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:52866600-52869800	Enhancers	Liver	Liver
22	chr3:52866600-52869800	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
24	chr3:52866600-52879200	Weak transcription	Osteobl	bone
25	chr3:52866800-52871000	Strong transcription	Spleen	Spleen
26	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
29	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
30	chr3:52867000-52870600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:52867000-52871000	Strong transcription	Thymus	Thymus
32	chr3:52867000-52871200	Weak transcription	Pancreas	Pancrea
33	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:52867200-52871400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:52867400-52870000	Flanking Active TSS	Fetal Muscle Trunk	muscle
39	chr3:52867600-52871800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:52867800-52870600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:52867800-52871200	Enhancers	Right Ventricle	heart
42	chr3:52868000-52869600	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:52868200-52869600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:52868200-52870000	Enhancers	Fetal Lung	lung
47	chr3:52868200-52870200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:52868400-52869400	Active TSS	Colonic Mucosa	Colon
49	chr3:52868400-52869400	Active TSS	Psoas Muscle	Psoas
50	chr3:52868400-52869400	Active TSS	Rectal Mucosa Donor 29	rectum

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