Variant report

Variant	rs2939523
Chromosome Location	chr5:145658068-145658069
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 175 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10491259	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs10491260	0.86[CHB][hapmap]
rs10491261	0.86[CHB][hapmap]
rs10515565	0.88[CEU][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10515566	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10515567	0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1054020	0.86[CHB][hapmap]
rs1115080	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11167932	0.84[CHB][hapmap]
rs11167937	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11948314	0.86[CHB][hapmap]
rs11952445	0.94[ASN][1000 genomes]
rs11953090	0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs11953506	0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11953517	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs11954297	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11954750	0.85[CHB][hapmap]
rs11954977	0.86[CHB][hapmap]
rs11955206	0.94[ASN][1000 genomes]
rs11957907	0.85[ASN][1000 genomes]
rs11957998	0.86[CHB][hapmap]
rs11958136	0.88[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11958633	0.83[ASN][1000 genomes]
rs12152830	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12153109	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs12153364	0.85[ASN][1000 genomes]
rs12186358	0.86[CHB][hapmap]
rs12187277	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12187913	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs12188581	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs12189077	0.94[ASN][1000 genomes]
rs12189385	0.86[CHB][hapmap]
rs13153675	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs13153891	0.90[ASN][1000 genomes]
rs13154219	0.92[ASN][1000 genomes]
rs13155119	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs13157784	0.81[ASN][1000 genomes]
rs13160605	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13160905	0.89[ASN][1000 genomes]
rs13161488	0.82[AMR][1000 genomes]
rs13161659	0.85[CHB][hapmap]
rs13164872	0.85[ASN][1000 genomes]
rs13168967	0.89[ASN][1000 genomes]
rs13169370	0.90[ASN][1000 genomes]
rs13169390	0.91[ASN][1000 genomes]
rs13171939	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13173347	0.91[ASN][1000 genomes]
rs13173462	0.83[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs13177015	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13178370	0.86[CHB][hapmap]
rs13178443	0.90[ASN][1000 genomes]
rs13178516	0.86[CHB][hapmap]
rs13178840	0.85[CHB][hapmap]
rs13180255	0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs13181074	0.86[CHB][hapmap]
rs13182302	0.86[CHB][hapmap]
rs13182567	0.86[CHB][hapmap]
rs13182948	0.83[ASN][1000 genomes]
rs13183541	0.90[ASN][1000 genomes]
rs13183976	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13185518	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13186694	0.85[CHB][hapmap]
rs1368345	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1395277	0.85[CHB][hapmap]
rs1567057	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17096590	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17427286	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs17427691	0.85[CHB][hapmap]
rs17428100	0.85[CHB][hapmap]
rs17428465	0.86[CHB][hapmap]
rs17428570	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs17428724	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs17429180	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17443315	0.85[ASN][1000 genomes]
rs17492851	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs17492893	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs17492950	0.85[CHB][hapmap]
rs17493090	0.85[CHB][hapmap]
rs17500483	0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[TSI][hapmap]
rs17500504	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs17501177	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs17501601	0.92[ASN][1000 genomes]
rs17502157	0.94[ASN][1000 genomes]
rs17502233	0.93[ASN][1000 genomes]
rs17502345	0.93[ASN][1000 genomes]
rs17687490	0.93[ASN][1000 genomes]
rs1864948	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1911112	0.85[CHB][hapmap]
rs1911113	0.85[CHB][hapmap]
rs2014462	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2014469	0.85[ASN][1000 genomes]
rs2014473	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2053045	0.84[ASN][1000 genomes]
rs2063002	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2063005	0.83[MEX][hapmap]
rs2116749	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2279895	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2304032	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304033	0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2400211	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2895647	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2895648	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2895649	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs2939536	0.86[CHB][hapmap]
rs2962502	0.84[CHB][hapmap]
rs2962511	0.85[CHB][hapmap];0.87[CHD][hapmap];0.84[TSI][hapmap]
rs2963914	0.86[CHB][hapmap]
rs2963915	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[TSI][hapmap]
rs2963919	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[TSI][hapmap]
rs2963921	0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2963926	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34082425	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34141601	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34170515	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs34444119	0.89[ASN][1000 genomes]
rs34775587	0.94[ASN][1000 genomes]
rs34812645	0.88[ASN][1000 genomes]
rs34819107	0.83[ASN][1000 genomes]
rs34993855	0.85[ASN][1000 genomes]
rs35170264	0.85[ASN][1000 genomes]
rs35369194	0.83[EUR][1000 genomes]
rs35575652	0.94[ASN][1000 genomes]
rs35870798	0.94[ASN][1000 genomes]
rs35935643	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35947468	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36019024	0.89[ASN][1000 genomes]
rs3749994	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs3763373	0.83[CHD][hapmap]
rs3797628	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs3822623	0.85[CHB][hapmap]
rs3828935	0.83[CHD][hapmap]
rs3937558	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41338847	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4413574	0.86[CHB][hapmap]
rs4705156	0.88[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705157	0.92[ASN][1000 genomes]
rs4705179	0.86[CHB][hapmap];0.96[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4913064	0.86[CHB][hapmap]
rs55937908	0.91[ASN][1000 genomes]
rs56413906	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58848845	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62372766	0.89[ASN][1000 genomes]
rs62372767	0.86[ASN][1000 genomes]
rs62372768	0.94[ASN][1000 genomes]
rs62372769	0.94[ASN][1000 genomes]
rs62372772	0.94[ASN][1000 genomes]
rs62372773	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62373831	0.88[ASN][1000 genomes]
rs6580413	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6867146	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868728	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6870878	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6877277	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs6878005	0.87[CEU][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6881180	0.84[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6882517	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884493	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6893994	0.82[ASN][1000 genomes]
rs7443214	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs7702123	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703269	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7722258	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7724811	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7727353	0.85[ASN][1000 genomes]
rs7728381	0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs7729098	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9918101	0.80[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883006	chr5:145450586-145672431	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428128	chr5:145503978-145682880	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv883007	chr5:145506100-145672431	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv883009	chr5:145567877-145672431	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv883011	chr5:145583623-145672431	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv883012	chr5:145589542-145672431	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv462478	chr5:145622472-145687295	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	nsv599937	chr5:145622472-145687295	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2939523	PLAC8L1	cis	parietal	SCAN
rs2939523	LARS	Cis_1M	lymphoblastoid	RTeQTL
rs2939523	LARS	cis	parietal	SCAN
rs2939523	LARS	cis	cerebellum	SCAN
rs2939523	LARS	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145597000-145668400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:145611200-145670600	Weak transcription	Small Intestine	intestine
3	chr5:145613400-145658800	Weak transcription	Pancreas	Pancrea
4	chr5:145621000-145664600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:145623000-145667800	Strong transcription	Dnd41	blood
6	chr5:145624800-145665200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:145628200-145669000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:145630600-145667000	Strong transcription	Fetal Thymus	thymus
9	chr5:145630600-145667400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr5:145630800-145658800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:145630800-145667200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:145630800-145668400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:145630800-145669600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:145631000-145668400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:145631200-145662600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:145631200-145669000	Strong transcription	Liver	Liver
17	chr5:145633000-145669400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:145633800-145667200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:145639400-145662400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:145640000-145662000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:145641400-145663000	Weak transcription	Right Ventricle	heart
22	chr5:145641400-145668000	Weak transcription	Gastric	stomach
23	chr5:145641600-145658800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:145641600-145670600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:145641800-145658400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr5:145642400-145659800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:145642400-145667400	Weak transcription	Brain Angular Gyrus	brain
28	chr5:145642800-145662800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:145642800-145662800	Weak transcription	Aorta	Aorta
30	chr5:145643600-145664400	Weak transcription	Lung	lung
31	chr5:145644000-145662800	Weak transcription	HSMMtube	muscle
32	chr5:145644400-145658800	Strong transcription	K562	blood
33	chr5:145645200-145663200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:145645200-145664800	Strong transcription	Fetal Intestine Large	intestine
35	chr5:145645600-145662400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:145645600-145667200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:145647200-145666600	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr5:145649200-145676200	Weak transcription	Fetal Brain Male	brain
39	chr5:145649600-145661200	Weak transcription	Ovary	ovary
40	chr5:145649600-145663200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr5:145651200-145659000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:145651200-145665800	Weak transcription	Fetal Kidney	kidney
43	chr5:145651400-145660000	Weak transcription	NH-A	brain
44	chr5:145651400-145662000	Weak transcription	GM12878-XiMat	blood
45	chr5:145651400-145662800	Weak transcription	NHLF	lung
46	chr5:145651400-145663600	Weak transcription	Stomach Mucosa	stomach
47	chr5:145651600-145662800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:145652000-145659600	Weak transcription	Hela-S3	cervix
49	chr5:145652000-145660000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr5:145652000-145661800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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