Variant report

Variant	rs6151816
Chromosome Location	chr5:80073634-80073635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12513549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13154537	0.82[EUR][1000 genomes]
rs2306371	0.82[EUR][1000 genomes]
rs2897298	0.86[GIH][hapmap];0.86[MEX][hapmap]
rs34341204	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35688814	0.82[EUR][1000 genomes]
rs6151809	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6151816	MSH3	cis	parietal	SCAN
rs6151816	MSH3	cis	lymphoblastoid	seeQTL
rs6151816	MSH3	cis	cerebellum	SCAN
rs6151816	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 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	chr5:80039200-80075800	Weak transcription	HepG2	liver
5	chr5:80040200-80073800	Weak transcription	Hela-S3	cervix
6	chr5:80041200-80076000	Weak transcription	Small Intestine	intestine
7	chr5:80041200-80100400	Weak transcription	Gastric	stomach
8	chr5:80041800-80094200	Weak transcription	NHLF	lung
9	chr5:80042200-80075800	Weak transcription	A549	lung
10	chr5:80042800-80074800	Weak transcription	Fetal Stomach	stomach
11	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
13	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
14	chr5:80043000-80075600	Weak transcription	Ovary	ovary
15	chr5:80043200-80075800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:80043400-80076200	Weak transcription	HUVEC	blood vessel
17	chr5:80043600-80089000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
19	chr5:80048800-80088000	Weak transcription	Fetal Kidney	kidney
20	chr5:80049400-80089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:80049600-80077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:80049800-80088800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:80051000-80078600	Weak transcription	NHDF-Ad	bronchial
24	chr5:80051200-80075000	Weak transcription	Osteobl	bone
25	chr5:80051200-80077000	Weak transcription	NH-A	brain
26	chr5:80051200-80084000	Weak transcription	Thymus	Thymus
27	chr5:80051600-80075800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:80051600-80088600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:80051600-80088800	Weak transcription	Colonic Mucosa	Colon
30	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
31	chr5:80051800-80075000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:80051800-80089000	Weak transcription	HSMMtube	muscle
33	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
34	chr5:80052400-80075600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:80052400-80075800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr5:80052400-80085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:80053000-80075800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:80053000-80088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:80056600-80075000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:80056800-80089000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:80057000-80085600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:80057200-80075800	Weak transcription	Fetal Intestine Large	intestine
43	chr5:80057200-80083800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:80057200-80088000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:80057200-80090000	Weak transcription	Aorta	Aorta
46	chr5:80057200-80094200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:80057400-80089200	Weak transcription	K562	blood
48	chr5:80057600-80074800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:80058000-80076800	Weak transcription	NHEK	skin
50	chr5:80058000-80089000	Weak transcription	Brain Hippocampus Middle	brain

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