Variant report

Variant	rs960739
Chromosome Location	chr4:119651705-119651706
allele	C/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	FAM48A	chr4:119651589-119651725	GM12878	blood:	n/a	n/a
2	MAFK	chr4:119650852-119651882	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
SEC24D	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10011981	0.85[YRI][hapmap]
rs10014208	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs10018497	0.85[YRI][hapmap]
rs10031357	0.82[YRI][hapmap]
rs10470914	0.84[JPT][hapmap]
rs10518322	0.91[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs10518323	0.91[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs10518324	0.91[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs11098450	0.91[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs11722833	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730993	0.83[AMR][1000 genomes]
rs11736024	0.88[GIH][hapmap];0.82[JPT][hapmap]
rs12500272	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12505513	0.87[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs12509236	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12509654	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13109947	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13109966	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13114964	0.91[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13120798	0.91[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs13128195	0.82[JPT][hapmap]
rs13130107	0.95[EUR][1000 genomes]
rs17050423	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs298976	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs298977	0.95[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs298980	0.95[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs298981	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs298989	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs298990	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298993	0.96[EUR][1000 genomes]
rs298997	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs299002	0.94[EUR][1000 genomes]
rs299003	0.94[EUR][1000 genomes]
rs299004	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs34371874	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs34384498	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34616305	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34730066	0.82[AMR][1000 genomes]
rs35868882	0.81[AMR][1000 genomes]
rs3775836	0.89[GIH][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs399086	0.94[EUR][1000 genomes]
rs401950	0.93[EUR][1000 genomes]
rs428409	0.95[EUR][1000 genomes]
rs437027	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs439159	0.94[EUR][1000 genomes]
rs4834698	0.95[EUR][1000 genomes]
rs4834699	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7676832	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs960738	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs960739	USP53	cis	cerebellum	SCAN
rs960739	METTL14	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
4	chr4:119620000-119660200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
6	chr4:119628000-119659800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:119628400-119657600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:119630400-119674200	Weak transcription	A549	lung
9	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
10	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
11	chr4:119634400-119660000	Weak transcription	Brain Angular Gyrus	brain
12	chr4:119640600-119662200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:119641200-119652600	Strong transcription	HSMMtube	muscle
15	chr4:119641200-119659600	Strong transcription	Fetal Intestine Large	intestine
16	chr4:119641600-119659400	Strong transcription	Liver	Liver
17	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr4:119642000-119653200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:119642000-119653400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:119642000-119654400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr4:119642000-119661200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:119642000-119662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:119642000-119662000	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
25	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
26	chr4:119642400-119656400	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr4:119642400-119662000	Strong transcription	Adipose Nuclei	Adipose
28	chr4:119642400-119662000	Strong transcription	Fetal Lung	lung
29	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:119643000-119658400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:119643000-119662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:119643200-119653600	Strong transcription	HMEC	breast
33	chr4:119644200-119659600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:119644400-119652600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr4:119644400-119653800	Strong transcription	NHEK	skin
36	chr4:119644400-119655000	Strong transcription	Dnd41	blood
37	chr4:119644400-119662000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:119644400-119662000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:119644600-119654400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:119644800-119654400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:119645200-119653600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr4:119645400-119654000	Strong transcription	Rectal Smooth Muscle	rectum
44	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:119645800-119654400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:119645800-119654400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:119646000-119651800	Strong transcription	K562	blood
48	chr4:119646000-119652800	Strong transcription	Primary B cells from cord blood	blood
49	chr4:119646000-119654400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:119646000-119654400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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