Variant report

Variant	rs1805353
Chromosome Location	chr5:80160610-80160611
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10040849	0.87[ASN][1000 genomes]
rs10075024	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16878166	0.87[ASN][1000 genomes]
rs16878216	0.81[EUR][1000 genomes]
rs28831684	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56103733	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61171552	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6151838	0.87[ASN][1000 genomes]
rs6151900	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151925	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151927	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151935	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73125413	0.87[ASN][1000 genomes]
rs73125416	0.87[ASN][1000 genomes]
rs73127211	0.93[ASN][1000 genomes]
rs73137538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139506	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73139515	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs964584	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[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	esv3410344	chr5:80160551-80160818	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1805353	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
2	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
4	chr5:80125200-80161600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr5:80141200-80161000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr5:80141200-80178800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:80143000-80175400	Weak transcription	HMEC	breast
8	chr5:80145600-80172800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr5:80145600-80175600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:80145600-80181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:80145800-80167400	Weak transcription	Placenta	Placenta
12	chr5:80145800-80173400	Weak transcription	Colonic Mucosa	Colon
13	chr5:80146000-80173400	Weak transcription	Esophagus	oesophagus
14	chr5:80146400-80162600	Weak transcription	Fetal Stomach	stomach
15	chr5:80146400-80162800	Weak transcription	Gastric	stomach
16	chr5:80146400-80167200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:80146400-80167200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:80146400-80170600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:80146400-80173400	Weak transcription	Brain Substantia Nigra	brain
20	chr5:80146600-80162000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:80146800-80161600	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:80146800-80161800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:80148400-80167400	Weak transcription	HSMM	muscle
24	chr5:80148600-80175600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:80148800-80173200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:80149000-80161800	Weak transcription	HepG2	liver
27	chr5:80149200-80166000	Weak transcription	K562	blood
28	chr5:80149200-80167200	Weak transcription	Hela-S3	cervix
29	chr5:80149200-80176200	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:80149800-80180000	Weak transcription	Psoas Muscle	Psoas
31	chr5:80151200-80173000	Weak transcription	Fetal Brain Male	brain
32	chr5:80151400-80161800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:80151600-80162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:80151600-80175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:80151800-80162600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:80152000-80160800	Weak transcription	Ovary	ovary
37	chr5:80152000-80161800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:80152000-80167000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:80152000-80167200	Weak transcription	Aorta	Aorta
40	chr5:80152000-80170800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:80152000-80171000	Weak transcription	Lung	lung
42	chr5:80152000-80173400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:80152000-80173400	Weak transcription	Pancreas	Pancrea
44	chr5:80152000-80173400	Weak transcription	Thymus	Thymus
45	chr5:80152200-80161000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr5:80152200-80161600	Weak transcription	Left Ventricle	heart
47	chr5:80152200-80170800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:80152800-80173200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:80152800-80179000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr5:80153000-80161000	Weak transcription	Liver	Liver

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