Variant report

Variant	rs26782
Chromosome Location	chr5:80052419-80052420
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80048062..80050226-chr5:80052118..80053918,2	MCF-7	breast:
2	chr5:80049158..80052845-chr5:80056288..80059425,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs151886	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245009	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs245014	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs245398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245404	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26780	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26781	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28059	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs32951	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32953	0.93[EUR][1000 genomes]
rs32960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33008	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33011	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3776972	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40592	0.81[EUR][1000 genomes]
rs41097	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151706	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151707	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857288	0.82[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs26782	DHFR	cis	Muscle Skeletal	GTEx
rs26782	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
4	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:80039200-80075800	Weak transcription	HepG2	liver
6	chr5:80039400-80060200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:80040200-80073800	Weak transcription	Hela-S3	cervix
8	chr5:80041200-80076000	Weak transcription	Small Intestine	intestine
9	chr5:80041200-80100400	Weak transcription	Gastric	stomach
10	chr5:80041800-80055200	Weak transcription	Esophagus	oesophagus
11	chr5:80041800-80094200	Weak transcription	NHLF	lung
12	chr5:80042200-80075800	Weak transcription	A549	lung
13	chr5:80042400-80056800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:80042800-80055600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:80042800-80056600	Weak transcription	Aorta	Aorta
16	chr5:80042800-80056600	Weak transcription	Fetal Lung	lung
17	chr5:80042800-80057000	Weak transcription	NHEK	skin
18	chr5:80042800-80068600	Weak transcription	Pancreas	Pancrea
19	chr5:80042800-80073400	Weak transcription	Fetal Intestine Small	intestine
20	chr5:80042800-80074800	Weak transcription	Fetal Stomach	stomach
21	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
22	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
23	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
24	chr5:80043000-80056600	Weak transcription	Fetal Intestine Large	intestine
25	chr5:80043000-80057000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:80043000-80059200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:80043000-80067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:80043000-80073600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:80043000-80075600	Weak transcription	Ovary	ovary
30	chr5:80043200-80075800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr5:80043400-80076200	Weak transcription	HUVEC	blood vessel
32	chr5:80043600-80089000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr5:80043800-80057000	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:80043800-80059200	Weak transcription	Fetal Brain Female	brain
35	chr5:80044000-80056200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:80044000-80059000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
38	chr5:80044400-80073600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:80045200-80059000	Weak transcription	Lung	lung
40	chr5:80045400-80063200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:80045800-80056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr5:80048800-80088000	Weak transcription	Fetal Kidney	kidney
43	chr5:80049000-80052600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr5:80049200-80052800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:80049400-80052600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:80049400-80057000	Weak transcription	Adipose Nuclei	Adipose
47	chr5:80049400-80089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:80049600-80053800	Weak transcription	Liver	Liver
49	chr5:80049600-80054800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:80049600-80077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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