Variant report

Variant	rs2389885
Chromosome Location	chr4:120533931-120533932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120532371..120535379-chr4:120540193..120542602,3	K562	blood:

Extended variants
information (count: 126 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10008791	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10009566	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10009626	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10012252	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10013305	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10018280	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10019674	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10022185	0.84[EUR][1000 genomes]
rs10030660	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10034450	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10050092	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1010739	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1010740	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098531	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11098532	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11098534	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1155576	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11723090	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11731756	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11736416	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11737395	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11933966	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11947234	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12498539	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12498599	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12499377	0.81[EUR][1000 genomes]
rs12502389	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12504773	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12505735	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512646	0.80[EUR][1000 genomes]
rs12642411	0.81[EUR][1000 genomes]
rs13122709	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13128602	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13134665	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13136462	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13140391	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13140409	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13149407	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1383532	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1383533	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1480936	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480939	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1480940	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552092	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1552095	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17050695	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17051352	0.81[EUR][1000 genomes]
rs2086450	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2127823	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2170276	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291185	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2306456	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306457	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389880	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2389882	0.84[EUR][1000 genomes]
rs2389886	0.84[EUR][1000 genomes]
rs2389887	0.84[EUR][1000 genomes]
rs28394116	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28535956	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28578366	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28718422	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28735358	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28787668	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28850368	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34278750	0.82[EUR][1000 genomes]
rs34308924	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34835603	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34868248	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35111518	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36040693	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3733525	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736115	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756156	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3775841	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775843	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3775844	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775845	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775847	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775848	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775849	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3775852	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3775854	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3775858	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3806808	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822190	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3822191	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3822192	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3822194	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822195	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4504231	0.81[EUR][1000 genomes]
rs4596225	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4998488	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55825515	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58452170	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59732491	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6534139	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6534140	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6534141	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6829903	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6832740	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6833334	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6835635	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6847818	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6853998	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6855918	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6858592	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6858777	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7664986	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7669520	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7676296	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7678400	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7680063	0.81[EUR][1000 genomes]
rs7680914	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7688802	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7693919	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695292	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7695620	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7699064	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9884402	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9995026	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9997631	0.87[EUR][1000 genomes];0.84[ASN][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1006572	chr4:120432494-120694243	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2389885	RP11-33B1.1	cis	Whole Blood	GTEx
rs2389885	RP11-33B1.1	cis	lung	GTEx
rs2389885	RP11-33B1.1	cis	Esophagus Mucosa	GTEx
rs2389885	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs2389885	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs2389885	RP11-33B1.4	cis	Whole Blood	GTEx
rs2389885	RP11-33B1.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120492200-120540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:120502600-120541000	Weak transcription	Left Ventricle	heart
3	chr4:120517000-120536600	Weak transcription	Ovary	ovary
4	chr4:120518800-120547200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:120520200-120536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:120520400-120537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:120521000-120544800	Weak transcription	Fetal Intestine Large	intestine
8	chr4:120525800-120538800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:120526200-120546800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:120526400-120544200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:120526600-120535400	Weak transcription	Fetal Brain Male	brain
12	chr4:120527400-120536400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:120528400-120547400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:120528600-120547400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:120528600-120547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:120528800-120539000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:120528800-120540200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:120528800-120543000	Weak transcription	Pancreas	Pancrea
19	chr4:120528800-120544200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:120528800-120545400	Weak transcription	Fetal Stomach	stomach
21	chr4:120529000-120546600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:120531600-120534800	Strong transcription	Osteobl	bone
23	chr4:120532000-120534000	Strong transcription	NHLF	lung
24	chr4:120532000-120536200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:120532200-120535600	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:120532200-120536000	Weak transcription	Aorta	Aorta
27	chr4:120532400-120536600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr4:120532400-120547600	Weak transcription	Lung	lung
29	chr4:120533000-120544200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:120533200-120534000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:120533400-120534000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:120533600-120535800	Weak transcription	Fetal Lung	lung
33	chr4:120533600-120539200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:120533600-120547400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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