Variant report

Variant	rs12513549
Chromosome Location	chr5:80077128-80077129
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80067813..80071581-chr5:80076574..80078808,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13154537	0.88[EUR][1000 genomes]
rs2306371	0.88[EUR][1000 genomes]
rs2897298	0.86[GIH][hapmap];0.86[MEX][hapmap]
rs34341204	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35688814	0.88[EUR][1000 genomes]
rs6151809	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12513549	MSH3	cis	parietal	SCAN
rs12513549	MSH3	cis	cerebellum	SCAN
rs12513549	DP58	cis	multi-tissue	Pritchard
rs12513549	MSH3	cis	multi-tissue	Pritchard
rs12513549	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs12513549	MSH3	cis	lymphoblastoid	seeQTL

Chromatin state (count:108 , 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	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80041200-80100400	Weak transcription	Gastric	stomach
5	chr5:80041800-80094200	Weak transcription	NHLF	lung
6	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
7	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
8	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
9	chr5:80043600-80089000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
11	chr5:80048800-80088000	Weak transcription	Fetal Kidney	kidney
12	chr5:80049400-80089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:80049800-80088800	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:80051000-80078600	Weak transcription	NHDF-Ad	bronchial
15	chr5:80051200-80084000	Weak transcription	Thymus	Thymus
16	chr5:80051600-80088600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:80051600-80088800	Weak transcription	Colonic Mucosa	Colon
18	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
19	chr5:80051800-80089000	Weak transcription	HSMMtube	muscle
20	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
21	chr5:80052400-80085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:80053000-80088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:80056800-80089000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:80057000-80085600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:80057200-80083800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:80057200-80088000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:80057200-80090000	Weak transcription	Aorta	Aorta
28	chr5:80057200-80094200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:80057400-80089200	Weak transcription	K562	blood
30	chr5:80058000-80089000	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:80059400-80088600	Weak transcription	Fetal Brain Female	brain
32	chr5:80059600-80089200	Weak transcription	Lung	lung
33	chr5:80059800-80085400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:80064400-80088600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:80064600-80088800	Weak transcription	HSMM	muscle
36	chr5:80064800-80089200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:80068800-80077200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:80069000-80093600	Weak transcription	Pancreas	Pancrea
39	chr5:80069400-80089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:80070200-80086000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:80071800-80077400	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:80072000-80079600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr5:80072200-80077800	Strong transcription	Liver	Liver
44	chr5:80072200-80081200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:80072800-80089000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:80073000-80077200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:80073200-80077200	Weak transcription	GM12878-XiMat	blood
48	chr5:80073200-80093600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:80073600-80089200	Weak transcription	H9 Cell Line	embryonic stem cell

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