Variant report

Variant	rs12522063
Chromosome Location	chr5:80187929-80187930
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	chr5:80187844..80190265-chr5:80191742..80193498,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10057510	0.85[AFR][1000 genomes]
rs1008119	0.86[ASN][1000 genomes]
rs10942930	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942931	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942932	0.89[ASN][1000 genomes]
rs12521082	0.90[ASN][1000 genomes]
rs1363365	0.90[ASN][1000 genomes]
rs1428030	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs16878204	0.84[ASN][1000 genomes]
rs1979005	0.93[ASN][1000 genomes]
rs2112416	0.90[ASN][1000 genomes]
rs3776969	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs3797885	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs3797886	0.85[CHD][hapmap]
rs3797897	0.92[ASN][1000 genomes]
rs4703819	0.84[ASN][1000 genomes]
rs4704686	0.93[ASN][1000 genomes]
rs4704687	0.93[ASN][1000 genomes]
rs4704690	0.82[ASN][1000 genomes]
rs55928960	0.84[ASN][1000 genomes]
rs56382955	0.98[ASN][1000 genomes]
rs57067128	0.83[ASN][1000 genomes]
rs58508689	0.91[ASN][1000 genomes]
rs6151826	0.90[JPT][hapmap]
rs6151865	0.80[ASN][1000 genomes]
rs6151892	0.83[ASN][1000 genomes]
rs6151901	0.91[ASN][1000 genomes]
rs6151909	0.84[ASN][1000 genomes]
rs6864713	0.97[ASN][1000 genomes]
rs6869680	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6885935	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6894961	0.80[ASN][1000 genomes]
rs71636250	0.86[AFR][1000 genomes]
rs72765588	0.89[ASN][1000 genomes]
rs72765590	0.83[ASN][1000 genomes]
rs72765599	0.93[ASN][1000 genomes]
rs72767343	0.96[ASN][1000 genomes]
rs73137557	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12522063	MSH3	cis	parietal	SCAN
rs12522063	ZFYVE16	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80163200-80188400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:80169600-80190600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:80171400-80196400	Weak transcription	Hela-S3	cervix
4	chr5:80173600-80208000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:80173800-80188600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr5:80174000-80188200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:80174000-80188400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:80174000-80188400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:80174000-80188600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:80174000-80188600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:80174000-80190200	Weak transcription	Brain Anterior Caudate	brain
12	chr5:80174000-80190800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:80174000-80191200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:80174000-80191400	Weak transcription	Spleen	Spleen
15	chr5:80174000-80197000	Weak transcription	Left Ventricle	heart
16	chr5:80174200-80188000	Weak transcription	Brain Angular Gyrus	brain
17	chr5:80174200-80192000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:80180400-80191200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:80180400-80215000	Weak transcription	Fetal Kidney	kidney
20	chr5:80181600-80193200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:80181800-80188600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:80181800-80189400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:80181800-80189400	Weak transcription	A549	lung
24	chr5:80182000-80189400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:80182000-80191000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:80184200-80191800	Weak transcription	Gastric	stomach
27	chr5:80185800-80188000	Strong transcription	Primary B cells from cord blood	blood
28	chr5:80186800-80191000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:80187000-80188800	Weak transcription	Primary T cells from cord blood	blood
30	chr5:80187000-80197200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:80187200-80188800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:80187200-80189800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:80187200-80190200	Weak transcription	HSMMtube	muscle
34	chr5:80187200-80192000	Weak transcription	Fetal Stomach	stomach
35	chr5:80187200-80193400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:80187200-80194000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:80187200-80196400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr5:80187200-80197000	Weak transcription	Liver	Liver
39	chr5:80187200-80197200	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:80187400-80189000	Weak transcription	Adipose Nuclei	Adipose
41	chr5:80187400-80189000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:80187400-80190000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:80187400-80191000	Weak transcription	Dnd41	blood
44	chr5:80187400-80196800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr5:80187400-80197000	Weak transcription	Aorta	Aorta
46	chr5:80187400-80197000	Weak transcription	Thymus	Thymus
47	chr5:80187400-80197200	Weak transcription	Pancreas	Pancrea
48	chr5:80187800-80188000	Weak transcription	Fetal Intestine Small	intestine

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