Variant report

Variant	rs245369
Chromosome Location	chr5:80137400-80137401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10041898	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10057510	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs184967	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245337	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245339	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245344	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245347	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245350	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245352	0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245353	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245354	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245358	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245359	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245361	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245368	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs245370	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs245371	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245375	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245381	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245382	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245383	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245384	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs245387	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs245394	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245395	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs245396	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs245397	0.82[AMR][1000 genomes]
rs32965	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs32966	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs32980	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs32984	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs32987	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32994	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs32998	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33000	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33001	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35039937	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs39627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs40408	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41100	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6151616	0.82[GIH][hapmap];0.92[MEX][hapmap]
rs6869090	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6870306	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71636249	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71636250	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71636251	0.94[AMR][1000 genomes];0.96[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs245369	MSH3	cis	parietal	SCAN
rs245369	MSH3	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

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	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
5	chr5:80103800-80144600	Weak transcription	Gastric	stomach
6	chr5:80110600-80145200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:80119000-80145000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:80120800-80143800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:80125000-80141600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr5:80125000-80141600	Weak transcription	Ovary	ovary
11	chr5:80125000-80142000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:80125000-80142000	Weak transcription	Fetal Stomach	stomach
13	chr5:80125000-80142200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:80125000-80142200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:80125000-80142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:80125000-80143600	Weak transcription	Left Ventricle	heart
17	chr5:80125000-80143800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:80125000-80144600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr5:80125000-80145000	Weak transcription	Aorta	Aorta
20	chr5:80125200-80141600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:80125200-80142000	Weak transcription	Fetal Intestine Small	intestine
22	chr5:80125200-80143800	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:80125200-80144200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:80125200-80144400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:80125200-80144400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:80125200-80145000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:80125200-80145000	Weak transcription	Adipose Nuclei	Adipose
28	chr5:80125200-80145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:80125200-80151400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:80125400-80141800	Weak transcription	Liver	Liver
32	chr5:80125400-80143800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr5:80125400-80144200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:80125400-80145000	Weak transcription	HepG2	liver
35	chr5:80125400-80145200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:80125600-80144200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr5:80125800-80143800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:80125800-80145000	Weak transcription	Fetal Lung	lung
39	chr5:80128000-80145400	Weak transcription	Brain Substantia Nigra	brain
40	chr5:80130200-80142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:80134200-80143800	Weak transcription	Primary T cells from cord blood	blood
42	chr5:80134200-80144600	Weak transcription	Primary B cells from cord blood	blood
43	chr5:80135400-80145200	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:80136200-80137400	Weak transcription	Fetal Heart	heart
45	chr5:80136200-80145000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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