Variant report

Variant	rs13165877
Chromosome Location	chr5:80189933-80189934
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	chr5:80187844..80190265-chr5:80191742..80193498,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSH3-3	chr5:80189373-80190268	NONHSAT102421

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11950254	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11956599	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12515222	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12515548	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12518711	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12521191	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12521371	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12521389	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12521539	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12522132	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12522474	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12522866	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13168327	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13178429	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13178892	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13186354	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1679115	0.82[ASN][1000 genomes]
rs168653	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2112415	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306371	0.81[ASN][1000 genomes]
rs245340	0.89[ASN][1000 genomes]
rs245341	0.89[ASN][1000 genomes]
rs245348	0.85[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs245355	0.84[ASN][1000 genomes]
rs245356	0.84[ASN][1000 genomes]
rs245357	0.84[ASN][1000 genomes]
rs245360	0.84[ASN][1000 genomes]
rs245372	0.89[ASN][1000 genomes]
rs245373	0.82[ASN][1000 genomes]
rs245374	0.84[ASN][1000 genomes]
rs245379	0.82[ASN][1000 genomes]
rs245380	0.83[ASN][1000 genomes]
rs245385	0.84[ASN][1000 genomes]
rs245386	0.82[ASN][1000 genomes]
rs26278	0.82[ASN][1000 genomes]
rs26279	0.91[ASN][1000 genomes]
rs27366	0.83[ASN][1000 genomes]
rs27494	0.91[ASN][1000 genomes]
rs27887	0.91[ASN][1000 genomes]
rs2897298	0.91[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32963	0.91[ASN][1000 genomes]
rs32964	0.91[ASN][1000 genomes]
rs32967	0.91[ASN][1000 genomes]
rs32968	0.91[ASN][1000 genomes]
rs32969	0.82[ASN][1000 genomes]
rs32988	0.82[ASN][1000 genomes]
rs32989	0.82[ASN][1000 genomes]
rs34205517	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34274010	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34560430	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34799825	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34816304	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34829384	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34976588	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35109637	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35856198	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35889396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35967780	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36160284	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3776976	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3776977	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3776978	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3797898	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs39626	0.83[ASN][1000 genomes]
rs4293894	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55661202	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58825743	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59360125	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59568430	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151888	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6151896	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6151904	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151907	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6151919	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6151923	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66821541	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67240890	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6863363	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6874051	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6874652	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6877065	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6891635	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71636248	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72767323	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72767330	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7705816	0.92[ASN][1000 genomes]
rs7717404	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7721813	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7737445	0.93[ASN][1000 genomes]
rs888867	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9293824	0.97[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	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
3	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
4	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
5	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
6	esv1799323	chr5:80179312-80219650	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13165877	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80169600-80190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:80171400-80196400	Weak transcription	Hela-S3	cervix
3	chr5:80173600-80208000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80174000-80190200	Weak transcription	Brain Anterior Caudate	brain
5	chr5:80174000-80190800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:80174000-80191200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:80174000-80191400	Weak transcription	Spleen	Spleen
8	chr5:80174000-80197000	Weak transcription	Left Ventricle	heart
9	chr5:80174200-80192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:80180400-80191200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:80180400-80215000	Weak transcription	Fetal Kidney	kidney
12	chr5:80181600-80193200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:80182000-80191000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:80184200-80191800	Weak transcription	Gastric	stomach
15	chr5:80186800-80191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:80187000-80197200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:80187200-80190200	Weak transcription	HSMMtube	muscle
18	chr5:80187200-80192000	Weak transcription	Fetal Stomach	stomach
19	chr5:80187200-80193400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:80187200-80194000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:80187200-80196400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:80187200-80197000	Weak transcription	Liver	Liver
23	chr5:80187200-80197200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:80187400-80190000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:80187400-80191000	Weak transcription	Dnd41	blood
26	chr5:80187400-80196800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:80187400-80197000	Weak transcription	Aorta	Aorta
28	chr5:80187400-80197000	Weak transcription	Thymus	Thymus
29	chr5:80187400-80197200	Weak transcription	Pancreas	Pancrea
30	chr5:80188800-80190000	Strong transcription	Primary T cells from cord blood	blood
31	chr5:80189400-80190400	Enhancers	Fetal Heart	heart
32	chr5:80189600-80190600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:80189800-80190200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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