Variant report

Variant	rs3733324
Chromosome Location	chr4:57204960-57204961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11934636	1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs12640212	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12644498	0.81[JPT][hapmap]
rs12650288	1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs13102012	0.91[JPT][hapmap]
rs13124696	0.91[JPT][hapmap]
rs13134963	0.83[JPT][hapmap]
rs1579019	1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs17086759	0.94[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17086773	0.91[JPT][hapmap]
rs17086801	0.81[JPT][hapmap]
rs17086804	1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs17086830	0.80[JPT][hapmap]
rs17086838	0.81[JPT][hapmap]
rs2176785	0.83[JPT][hapmap]
rs2271924	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35854625	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3733326	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796539	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796540	0.93[CHB][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796550	1.00[ASW][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap]
rs4076103	0.81[JPT][hapmap]
rs41498446	1.00[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55778537	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55890437	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55903333	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55909588	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56095772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56129706	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56296497	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56406704	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57233429	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58654038	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59062367	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59153415	0.95[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59278715	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59764923	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6554347	0.91[JPT][hapmap]
rs6830145	0.81[JPT][hapmap]
rs7437839	0.95[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7694439	0.91[JPT][hapmap]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv3415289	chr4:57063312-57236755	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv829940	chr4:57072341-57262730	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3733324	SRP72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57167800-57218600	Weak transcription	Small Intestine	intestine
2	chr4:57177600-57215400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:57178200-57211800	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:57184600-57211200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:57190400-57214400	Weak transcription	Brain Anterior Caudate	brain
6	chr4:57190600-57214600	Weak transcription	Brain Substantia Nigra	brain
7	chr4:57190600-57252400	Weak transcription	Colonic Mucosa	Colon
8	chr4:57193600-57213000	Weak transcription	Left Ventricle	heart
9	chr4:57195000-57214400	Weak transcription	Placenta	Placenta
10	chr4:57195200-57238000	Weak transcription	HUVEC	blood vessel
11	chr4:57196000-57238200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:57198800-57214400	Weak transcription	Gastric	stomach
13	chr4:57201800-57212000	Weak transcription	Adipose Nuclei	Adipose
14	chr4:57202000-57212000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:57202600-57205000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
16	chr4:57202600-57205000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr4:57202600-57205000	Strong transcription	Fetal Intestine Large	intestine
18	chr4:57202600-57221400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr4:57202800-57205200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr4:57202800-57252400	Weak transcription	NHDF-Ad	bronchial
21	chr4:57203000-57205000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr4:57203000-57205200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr4:57203000-57205200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:57203000-57205200	Strong transcription	Brain Germinal Matrix	brain
25	chr4:57203000-57252600	Weak transcription	Right Ventricle	heart
26	chr4:57203200-57205000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
27	chr4:57203200-57205000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:57203200-57215000	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:57203200-57215600	Weak transcription	Pancreas	Pancrea
30	chr4:57203200-57235200	Weak transcription	Osteobl	bone
31	chr4:57203200-57251800	Weak transcription	A549	lung
32	chr4:57203400-57205000	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr4:57203400-57205200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:57203400-57212800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:57203400-57252400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:57203600-57205000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
37	chr4:57203600-57205200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:57203600-57205200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr4:57203600-57206400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:57203600-57213600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr4:57203600-57213600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:57203600-57214400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:57203600-57229400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr4:57203800-57205000	ZNF genes & repeats	Liver	Liver
45	chr4:57203800-57205000	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr4:57203800-57205200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr4:57203800-57205200	Strong transcription	Fetal Kidney	kidney
48	chr4:57203800-57205400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:57204000-57205000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:57204000-57205000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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