Variant report

Variant	rs245400
Chromosome Location	chr5:80047758-80047759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1650690	0.85[CEU][hapmap]
rs1650723	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs1650734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1650735	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1650736	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs245397	0.80[AMR][1000 genomes]
rs245399	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245403	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs245408	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs26266	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26268	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs26283	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs27365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs32958	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs32994	0.81[EUR][1000 genomes]
rs33009	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs33010	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs33012	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs39628	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs42290	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6151616	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs836790	1.00[CEU][hapmap];1.00[YRI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs245400	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs245400	MSH3	cis	Whole Blood	GTEx
rs245400	MSH3	cis	Thyroid	GTEx

Chromatin state (count:117 , 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	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
5	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
7	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
8	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:80033200-80051400	Weak transcription	HMEC	breast
10	chr5:80034200-80049400	Strong transcription	Primary T cells from cord blood	blood
11	chr5:80034800-80050600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:80035000-80050400	Weak transcription	Stomach Mucosa	stomach
13	chr5:80037200-80049800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr5:80037200-80050600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:80037400-80049000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:80037400-80050600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:80037600-80049000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:80037600-80050200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:80039200-80050200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:80039200-80051200	Weak transcription	Colonic Mucosa	Colon
21	chr5:80039200-80075800	Weak transcription	HepG2	liver
22	chr5:80039400-80060200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:80040200-80073800	Weak transcription	Hela-S3	cervix
24	chr5:80040400-80048600	Strong transcription	Primary B cells from cord blood	blood
25	chr5:80040600-80049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:80041000-80050200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr5:80041200-80050200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr5:80041200-80050400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:80041200-80076000	Weak transcription	Small Intestine	intestine
30	chr5:80041200-80100400	Weak transcription	Gastric	stomach
31	chr5:80041400-80049400	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:80041800-80055200	Weak transcription	Esophagus	oesophagus
33	chr5:80041800-80094200	Weak transcription	NHLF	lung
34	chr5:80042200-80048000	Weak transcription	Fetal Kidney	kidney
35	chr5:80042200-80049200	Weak transcription	Placenta	Placenta
36	chr5:80042200-80075800	Weak transcription	A549	lung
37	chr5:80042400-80050800	Weak transcription	Fetal Thymus	thymus
38	chr5:80042400-80051200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:80042400-80056800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:80042800-80055600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:80042800-80056600	Weak transcription	Aorta	Aorta
42	chr5:80042800-80056600	Weak transcription	Fetal Lung	lung
43	chr5:80042800-80057000	Weak transcription	NHEK	skin
44	chr5:80042800-80068600	Weak transcription	Pancreas	Pancrea
45	chr5:80042800-80073400	Weak transcription	Fetal Intestine Small	intestine
46	chr5:80042800-80074800	Weak transcription	Fetal Stomach	stomach
47	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
48	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
49	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
50	chr5:80043000-80050200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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