Variant report

Variant	rs245356
Chromosome Location	chr5:80145345-80145346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11950254	0.98[ASN][1000 genomes]
rs11956599	0.98[ASN][1000 genomes]
rs12515548	1.00[ASN][1000 genomes]
rs12518711	1.00[ASN][1000 genomes]
rs12521389	0.98[ASN][1000 genomes]
rs12521539	1.00[ASN][1000 genomes]
rs12522132	1.00[ASN][1000 genomes]
rs12522474	0.99[ASN][1000 genomes]
rs13154537	0.92[ASN][1000 genomes]
rs13165877	0.84[ASN][1000 genomes]
rs13168327	0.95[ASN][1000 genomes]
rs13178892	0.98[ASN][1000 genomes]
rs13179210	0.92[ASN][1000 genomes]
rs13186354	1.00[ASN][1000 genomes]
rs1679115	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168653	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112415	0.87[ASN][1000 genomes]
rs2306371	0.95[ASN][1000 genomes]
rs245340	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245341	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs245348	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245355	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245360	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245364	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245372	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs245373	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245374	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245379	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245380	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245385	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245386	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245389	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs245407	0.87[EUR][1000 genomes]
rs26278	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26279	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs27366	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27494	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs27887	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2897298	0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs32963	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32964	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32967	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32968	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32969	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32988	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32989	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32995	0.82[ASN][1000 genomes]
rs32999	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34205517	1.00[ASN][1000 genomes]
rs34274010	1.00[ASN][1000 genomes]
rs34560430	0.96[ASN][1000 genomes]
rs34799825	1.00[ASN][1000 genomes]
rs34816304	0.98[ASN][1000 genomes]
rs34976588	1.00[ASN][1000 genomes]
rs35109637	0.93[ASN][1000 genomes]
rs35688814	0.95[ASN][1000 genomes]
rs35856198	1.00[ASN][1000 genomes]
rs35889396	0.84[ASN][1000 genomes]
rs35967780	0.99[ASN][1000 genomes]
rs36160284	1.00[ASN][1000 genomes]
rs3776976	0.95[ASN][1000 genomes]
rs3776977	0.95[ASN][1000 genomes]
rs3776978	0.99[ASN][1000 genomes]
rs3797898	0.96[ASN][1000 genomes]
rs39626	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40591	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4293894	0.98[ASN][1000 genomes]
rs58825743	0.92[ASN][1000 genomes]
rs59360125	0.93[ASN][1000 genomes]
rs59568430	0.93[ASN][1000 genomes]
rs6151888	0.98[ASN][1000 genomes]
rs6151896	0.97[ASN][1000 genomes]
rs6151904	0.99[ASN][1000 genomes]
rs6151907	0.99[ASN][1000 genomes]
rs6151919	0.95[ASN][1000 genomes]
rs6151923	0.95[ASN][1000 genomes]
rs66821541	0.95[ASN][1000 genomes]
rs6863363	0.99[ASN][1000 genomes]
rs6874652	0.96[ASN][1000 genomes]
rs6877065	1.00[ASN][1000 genomes]
rs701388	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71636248	0.87[ASN][1000 genomes]
rs72767323	0.93[ASN][1000 genomes]
rs7705816	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7707965	0.85[ASN][1000 genomes]
rs7708096	0.93[ASN][1000 genomes]
rs7721813	0.98[ASN][1000 genomes]
rs888867	0.99[ASN][1000 genomes]
rs9293824	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs245356	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs245356	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 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	chr5:80125200-80145400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:80125200-80151400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:80128000-80145400	Weak transcription	Brain Substantia Nigra	brain
8	chr5:80137600-80152600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:80140400-80145400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr5:80140600-80145400	Weak transcription	Colonic Mucosa	Colon
11	chr5:80141000-80145800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:80141200-80161000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:80141200-80178800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:80141600-80148000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:80142000-80146600	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr5:80142000-80152600	Weak transcription	Brain Angular Gyrus	brain
17	chr5:80142400-80151200	Weak transcription	Ovary	ovary
18	chr5:80143000-80175400	Weak transcription	HMEC	breast
19	chr5:80143600-80146600	ZNF genes & repeats	Dnd41	blood
20	chr5:80143600-80146800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:80143600-80151400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:80143800-80145600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr5:80143800-80145600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr5:80143800-80145800	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:80143800-80146600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr5:80143800-80146800	Strong transcription	Primary T cells from cord blood	blood
27	chr5:80143800-80146800	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr5:80143800-80156600	Weak transcription	Osteobl	bone
29	chr5:80144200-80145400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr5:80144200-80145800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
31	chr5:80144400-80145400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
32	chr5:80144400-80145400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:80144400-80145600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:80144400-80145600	Strong transcription	Fetal Intestine Large	intestine
35	chr5:80144400-80145800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr5:80144400-80146200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:80144400-80146400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:80144400-80146400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr5:80144400-80146400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr5:80144400-80146600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr5:80144400-80146600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr5:80144400-80146800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr5:80144400-80147000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr5:80144400-80147200	ZNF genes & repeats	GM12878-XiMat	blood
45	chr5:80144600-80145400	Weak transcription	Left Ventricle	heart
46	chr5:80144600-80145600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:80144600-80145800	Strong transcription	Gastric	stomach
48	chr5:80144600-80146400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:80144600-80146600	ZNF genes & repeats	Primary B cells from cord blood	blood
50	chr5:80144600-80146800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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