Variant report

Variant	rs13154537
Chromosome Location	chr5:80106875-80106876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11950254	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11956599	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12513549	0.88[EUR][1000 genomes]
rs12515548	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12518711	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12521389	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12521539	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12522132	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12522474	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13168327	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13178892	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13179210	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13186354	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1679115	0.95[ASN][1000 genomes]
rs168653	0.91[ASN][1000 genomes]
rs2306371	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245340	0.87[ASN][1000 genomes]
rs245341	0.88[ASN][1000 genomes]
rs245348	0.91[ASN][1000 genomes]
rs245355	0.92[ASN][1000 genomes]
rs245356	0.92[ASN][1000 genomes]
rs245357	0.92[ASN][1000 genomes]
rs245360	0.92[ASN][1000 genomes]
rs245364	0.82[ASN][1000 genomes]
rs245372	0.88[ASN][1000 genomes]
rs245373	0.91[ASN][1000 genomes]
rs245374	0.93[ASN][1000 genomes]
rs245379	0.91[ASN][1000 genomes]
rs245380	0.89[ASN][1000 genomes]
rs245385	0.93[ASN][1000 genomes]
rs245386	0.91[ASN][1000 genomes]
rs245389	0.90[ASN][1000 genomes]
rs26278	0.95[ASN][1000 genomes]
rs26279	0.85[ASN][1000 genomes]
rs27366	0.90[ASN][1000 genomes]
rs27494	0.85[ASN][1000 genomes]
rs27887	0.85[ASN][1000 genomes]
rs2897298	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32963	0.85[ASN][1000 genomes]
rs32964	0.85[ASN][1000 genomes]
rs32967	0.85[ASN][1000 genomes]
rs32968	0.85[ASN][1000 genomes]
rs32988	0.95[ASN][1000 genomes]
rs32989	0.95[ASN][1000 genomes]
rs32995	0.83[ASN][1000 genomes]
rs32999	0.98[ASN][1000 genomes]
rs34205517	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34274010	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34341204	0.82[EUR][1000 genomes]
rs34560430	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34799825	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34816304	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34976588	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35109637	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35688814	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35856198	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35967780	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36160284	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776976	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776977	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776978	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797898	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs39626	0.94[ASN][1000 genomes]
rs40591	0.95[ASN][1000 genomes]
rs4293894	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58825743	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59360125	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59568430	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6151816	0.82[EUR][1000 genomes]
rs6151846	0.92[EUR][1000 genomes]
rs6151888	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6151896	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151904	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151907	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151919	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6151923	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66821541	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6863363	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6874652	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6877065	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs701388	0.87[ASN][1000 genomes]
rs72767323	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7707965	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7708096	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7721813	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs888867	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv882231	chr5:79984714-80187929	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13154537	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
4	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
5	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
7	chr5:80076200-80109600	Weak transcription	HepG2	liver
8	chr5:80077400-80108000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:80077600-80112000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:80088200-80109600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:80089400-80110400	Weak transcription	Hela-S3	cervix
16	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:80089600-80109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:80089600-80110200	Weak transcription	Brain Angular Gyrus	brain
20	chr5:80089600-80118400	Weak transcription	NHEK	skin
21	chr5:80089800-80112400	Weak transcription	K562	blood
22	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:80090000-80109400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:80090000-80111000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:80090200-80109200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:80090600-80109400	Weak transcription	HSMMtube	muscle
30	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:80091000-80109200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:80091000-80109200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:80091000-80109400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:80091000-80116600	Weak transcription	A549	lung
35	chr5:80091200-80109000	Weak transcription	HSMM	muscle
36	chr5:80091200-80109200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:80091200-80110600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:80091200-80116000	Weak transcription	Brain Substantia Nigra	brain
39	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:80091400-80109200	Weak transcription	Placenta	Placenta
41	chr5:80091400-80109200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:80091400-80109400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:80091400-80109400	Weak transcription	Fetal Thymus	thymus
44	chr5:80091400-80114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:80091400-80114800	Weak transcription	Thymus	Thymus
46	chr5:80091400-80117600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:80091400-80118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:80091400-80124600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:80091400-80124600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr5:80091400-80124600	Weak transcription	Rectal Smooth Muscle	rectum

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