Variant report

Variant	rs3774364
Chromosome Location	chr3:52863605-52863606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52860455..52862109-chr3:52862343..52864733,2	K562	blood:
2	chr3:52859743..52862109-chr3:52863233..52865763,2	K562	blood:

Variant related genes	Relation type
ENSG00000055955	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11715347	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719137	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11915546	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11918800	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11922961	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488303	0.84[ASN][1000 genomes]
rs13072536	0.84[ASN][1000 genomes]
rs2071040	0.84[ASN][1000 genomes]
rs2071041	0.84[ASN][1000 genomes]
rs2072391	0.84[ASN][1000 genomes]
rs2239547	0.83[ASN][1000 genomes]
rs2239548	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240915	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240917	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245538	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2245647	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2256332	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276815	0.84[ASN][1000 genomes]
rs2276817	0.84[ASN][1000 genomes]
rs2276823	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2336558	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2535633	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35004449	0.83[ASN][1000 genomes]
rs3755803	0.84[ASN][1000 genomes]
rs4687554	0.84[ASN][1000 genomes]
rs4687657	0.83[ASN][1000 genomes]
rs4687658	0.84[ASN][1000 genomes]
rs56019197	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60332615	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445541	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769789	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7617468	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7620690	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630552	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7652667	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3774364	ITIH4-AS1	cis	Artery Tibial	GTEx
rs3774364	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs3774364	ITIH4-AS1	cis	Artery Aorta	GTEx
rs3774364	ITIH4-AS1	cis	lung	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52848400-52865800	Weak transcription	Ovary	ovary
3	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
4	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
5	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
6	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
8	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:52855200-52865400	Weak transcription	Brain Substantia Nigra	brain
13	chr3:52855600-52865400	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:52856000-52865400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
16	chr3:52856200-52865600	Weak transcription	Left Ventricle	heart
17	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
18	chr3:52856600-52864400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:52857800-52865400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:52858200-52865400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:52858400-52865400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52858400-52865400	Weak transcription	Brain Angular Gyrus	brain
26	chr3:52858400-52866800	Weak transcription	Fetal Brain Female	brain
27	chr3:52858400-52867200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:52858600-52864600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:52858600-52864800	Weak transcription	Right Ventricle	heart
31	chr3:52858600-52865600	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:52858600-52866800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr3:52858600-52867000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:52858800-52864000	Weak transcription	Aorta	Aorta
35	chr3:52858800-52864400	Weak transcription	Placenta	Placenta
36	chr3:52858800-52866800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:52859000-52865200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:52859200-52865400	Weak transcription	Brain Anterior Caudate	brain
42	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
44	chr3:52860400-52865400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:52861000-52865000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:52861200-52865600	Weak transcription	Esophagus	oesophagus
47	chr3:52861200-52866400	Weak transcription	Primary T cells from cord blood	blood
48	chr3:52861200-52868800	Weak transcription	Lung	lung
49	chr3:52861600-52864200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:52861600-52865000	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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