Variant report

Variant	rs33013
Chromosome Location	chr5:80060016-80060017
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs151887	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2115014	1.00[CEU][hapmap]
rs245011	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs245012	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26778	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs26779	0.90[ASN][1000 genomes]
rs33008	0.83[TSI][hapmap]
rs33014	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33015	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380691	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.92[TSI][hapmap]
rs425463	0.82[CHD][hapmap]
rs6151617	0.85[CHB][hapmap]
rs6151627	0.86[TSI][hapmap]
rs6151653	0.86[TSI][hapmap]
rs857263	0.85[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	esv1795990	chr5:80043404-80066135	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs33013	DHFR	cis	multi-tissue	Pritchard
rs33013	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs33013	DHFR	cis	Muscle Skeletal	GTEx
rs33013	DHFR	cis	Esophagus Muscularis	GTEx
rs33013	DHFR	Cis_1M	lymphoblastoid	RTeQTL
rs33013	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs33013	MSH3	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

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	chr5:80039400-80060200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:80040200-80073800	Weak transcription	Hela-S3	cervix
7	chr5:80041200-80076000	Weak transcription	Small Intestine	intestine
8	chr5:80041200-80100400	Weak transcription	Gastric	stomach
9	chr5:80041800-80094200	Weak transcription	NHLF	lung
10	chr5:80042200-80075800	Weak transcription	A549	lung
11	chr5:80042800-80068600	Weak transcription	Pancreas	Pancrea
12	chr5:80042800-80073400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:80042800-80074800	Weak transcription	Fetal Stomach	stomach
14	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
15	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
16	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
17	chr5:80043000-80067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:80043000-80073600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:80043000-80075600	Weak transcription	Ovary	ovary
20	chr5:80043200-80075800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr5:80043400-80076200	Weak transcription	HUVEC	blood vessel
22	chr5:80043600-80089000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
24	chr5:80044400-80073600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:80045400-80063200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:80048800-80088000	Weak transcription	Fetal Kidney	kidney
27	chr5:80049400-80089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:80049600-80077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:80049800-80088800	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:80051000-80078600	Weak transcription	NHDF-Ad	bronchial
31	chr5:80051200-80064000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:80051200-80073600	Weak transcription	Left Ventricle	heart
33	chr5:80051200-80075000	Weak transcription	Osteobl	bone
34	chr5:80051200-80077000	Weak transcription	NH-A	brain
35	chr5:80051200-80084000	Weak transcription	Thymus	Thymus
36	chr5:80051400-80071800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:80051400-80073600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:80051600-80075800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr5:80051600-80088600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr5:80051600-80088800	Weak transcription	Colonic Mucosa	Colon
41	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
42	chr5:80051800-80075000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:80051800-80089000	Weak transcription	HSMMtube	muscle
44	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
45	chr5:80052400-80075600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr5:80052400-80075800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr5:80052400-80085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:80052800-80064000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:80052800-80072200	Weak transcription	GM12878-XiMat	blood
50	chr5:80053000-80075800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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