Variant report

Variant	rs2897298
Chromosome Location	chr5:80153476-80153477
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs11950254	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11956599	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12515222	0.89[EUR][1000 genomes]
rs12515548	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518711	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521191	0.87[EUR][1000 genomes]
rs12521371	0.84[EUR][1000 genomes]
rs12521389	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12521539	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522132	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522474	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522866	0.88[EUR][1000 genomes]
rs13154537	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13165877	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13168327	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13178429	0.85[EUR][1000 genomes]
rs13178892	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13179210	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13186354	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679115	0.97[ASN][1000 genomes]
rs168653	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2112415	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2306371	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245340	0.95[ASN][1000 genomes]
rs245341	0.96[ASN][1000 genomes]
rs245348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs245355	1.00[ASN][1000 genomes]
rs245356	1.00[ASN][1000 genomes]
rs245357	1.00[ASN][1000 genomes]
rs245360	1.00[ASN][1000 genomes]
rs245364	0.89[ASN][1000 genomes]
rs245372	0.94[ASN][1000 genomes]
rs245373	0.97[ASN][1000 genomes]
rs245374	0.99[ASN][1000 genomes]
rs245379	0.97[ASN][1000 genomes]
rs245380	0.95[ASN][1000 genomes]
rs245385	0.99[ASN][1000 genomes]
rs245386	0.97[ASN][1000 genomes]
rs245389	0.89[ASN][1000 genomes]
rs26278	0.97[ASN][1000 genomes]
rs26279	0.93[ASN][1000 genomes]
rs27366	0.98[ASN][1000 genomes]
rs27494	0.93[ASN][1000 genomes]
rs27887	0.93[ASN][1000 genomes]
rs32963	0.93[ASN][1000 genomes]
rs32964	0.93[ASN][1000 genomes]
rs32967	0.93[ASN][1000 genomes]
rs32968	0.93[ASN][1000 genomes]
rs32969	0.84[ASN][1000 genomes]
rs32988	0.97[ASN][1000 genomes]
rs32989	0.97[ASN][1000 genomes]
rs32995	0.82[ASN][1000 genomes]
rs32999	0.94[ASN][1000 genomes]
rs34205517	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34274010	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34560430	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34799825	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34816304	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34829384	0.83[EUR][1000 genomes]
rs34976588	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35109637	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35688814	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35856198	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35889396	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35967780	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36160284	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776976	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776977	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776978	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797898	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs39626	0.98[ASN][1000 genomes]
rs40591	0.94[ASN][1000 genomes]
rs4293894	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55661202	0.88[EUR][1000 genomes]
rs58825743	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59360125	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59568430	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151888	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6151896	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151904	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151907	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6151919	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6151923	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66821541	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67240890	0.88[EUR][1000 genomes]
rs6863363	0.92[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874051	0.88[EUR][1000 genomes]
rs6874652	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6877065	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891635	0.84[EUR][1000 genomes]
rs701388	0.93[ASN][1000 genomes]
rs71636248	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72767323	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72767330	0.88[EUR][1000 genomes]
rs7705816	0.80[ASN][1000 genomes]
rs7707965	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7708096	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7717404	0.88[EUR][1000 genomes]
rs7721813	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs888867	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293824	0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2897298	MSH3	cis	cerebellum	SCAN
rs2897298	MSH3	cis	parietal	SCAN
rs2897298	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
2	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
4	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:80141200-80161000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:80141200-80178800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:80143000-80175400	Weak transcription	HMEC	breast
8	chr5:80143800-80156600	Weak transcription	Osteobl	bone
9	chr5:80145600-80153800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:80145600-80157000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:80145600-80172800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr5:80145600-80175600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:80145600-80181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:80145800-80167400	Weak transcription	Placenta	Placenta
15	chr5:80145800-80173400	Weak transcription	Colonic Mucosa	Colon
16	chr5:80146000-80173400	Weak transcription	Esophagus	oesophagus
17	chr5:80146400-80162600	Weak transcription	Fetal Stomach	stomach
18	chr5:80146400-80162800	Weak transcription	Gastric	stomach
19	chr5:80146400-80167200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:80146400-80167200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:80146400-80170600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:80146400-80173400	Weak transcription	Brain Substantia Nigra	brain
23	chr5:80146600-80162000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:80146800-80161600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:80146800-80161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:80148400-80167400	Weak transcription	HSMM	muscle
27	chr5:80148600-80175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:80148800-80156800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:80148800-80173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:80149000-80161800	Weak transcription	HepG2	liver
31	chr5:80149200-80153800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:80149200-80157000	Weak transcription	HSMMtube	muscle
33	chr5:80149200-80166000	Weak transcription	K562	blood
34	chr5:80149200-80167200	Weak transcription	Hela-S3	cervix
35	chr5:80149200-80176200	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:80149800-80180000	Weak transcription	Psoas Muscle	Psoas
37	chr5:80150600-80154200	Strong transcription	Primary T cells from cord blood	blood
38	chr5:80150800-80156600	Weak transcription	Fetal Heart	heart
39	chr5:80151000-80153600	ZNF genes & repeats	GM12878-XiMat	blood
40	chr5:80151200-80173000	Weak transcription	Fetal Brain Male	brain
41	chr5:80151400-80153600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
42	chr5:80151400-80161800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:80151600-80162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:80151600-80175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:80151800-80153800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:80151800-80153800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
47	chr5:80151800-80162600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:80152000-80154000	Weak transcription	Fetal Intestine Small	intestine
49	chr5:80152000-80157000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:80152000-80157000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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