Variant report

Variant	rs245331
Chromosome Location	chr5:80026377-80026378
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10040849	0.87[ASN][1000 genomes]
rs11950902	1.00[ASN][1000 genomes]
rs1346463	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1346464	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1620258	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1643651	1.00[ASN][1000 genomes]
rs1650648	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1650688	0.88[ASN][1000 genomes]
rs1650737	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650742	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1650747	1.00[ASN][1000 genomes]
rs1650749	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1650750	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677630	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677652	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677653	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677654	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677655	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677707	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1677709	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16878166	0.87[ASN][1000 genomes]
rs245332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560425	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2618369	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs26267	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26282	0.89[EUR][1000 genomes]
rs28027	0.90[EUR][1000 genomes]
rs32959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6151615	1.00[ASN][1000 genomes]
rs6151665	1.00[ASN][1000 genomes]
rs6151770	1.00[ASN][1000 genomes]
rs6151838	0.87[ASN][1000 genomes]
rs73123307	0.88[ASN][1000 genomes]
rs73123310	1.00[ASN][1000 genomes]
rs73125413	0.87[ASN][1000 genomes]
rs73125416	0.87[ASN][1000 genomes]
rs73127211	0.80[ASN][1000 genomes]
rs836794	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs836795	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836798	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836799	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836800	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836801	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836802	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836804	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836806	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836808	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836809	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836810	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836813	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs836816	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844368	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs844369	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857016	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs861372	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs863214	0.81[AMR][1000 genomes];1.00[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs245331	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs245331	ANKRD34B	cis	Whole Blood	GTEx
rs245331	DHFR	cis	Whole Blood	GTEx
rs245331	MSH3	cis	Thyroid	GTEx
rs245331	DHFR	cis	Adipose Subcutaneous	GTEx
rs245331	DHFR	cis	Muscle Skeletal	GTEx
rs245331	MSH3	cis	Whole Blood	GTEx
rs245331	DHFR	cis	Heart Left Ventricle	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79963600-80038600	Weak transcription	Right Ventricle	heart
2	chr5:79964800-80057800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:79972400-80037000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
6	chr5:79998600-80051000	Weak transcription	Fetal Brain Male	brain
7	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:80000200-80038600	Weak transcription	Esophagus	oesophagus
9	chr5:80000400-80036800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:80000400-80036800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:80003600-80030400	Weak transcription	NHLF	lung
12	chr5:80004000-80026400	Weak transcription	Fetal Heart	heart
13	chr5:80004000-80050400	Weak transcription	NHDF-Ad	bronchial
14	chr5:80009800-80039000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:80010600-80036800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:80010800-80032400	Weak transcription	Stomach Mucosa	stomach
17	chr5:80015800-80032400	Weak transcription	Pancreas	Pancrea
18	chr5:80016000-80038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:80016000-80040600	Weak transcription	Small Intestine	intestine
20	chr5:80016200-80040600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:80016200-80040600	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:80016200-80043600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr5:80016400-80027800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:80016400-80032400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:80016400-80034200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:80016400-80038200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr5:80016400-80050800	Weak transcription	Psoas Muscle	Psoas
28	chr5:80016600-80034200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:80020200-80043600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:80020800-80030800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:80021200-80026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:80021200-80026400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:80021200-80026600	Strong transcription	Primary T cells from cord blood	blood
34	chr5:80021200-80026600	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr5:80021200-80026600	Strong transcription	Liver	Liver
36	chr5:80021200-80026600	Strong transcription	Placenta	Placenta
37	chr5:80021200-80026800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:80021200-80031000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:80021400-80026600	Strong transcription	Adipose Nuclei	Adipose
40	chr5:80022200-80032200	Weak transcription	A549	lung
41	chr5:80022200-80040000	Weak transcription	K562	blood
42	chr5:80022600-80034000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:80022800-80038000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:80022800-80038600	Weak transcription	Colonic Mucosa	Colon
45	chr5:80022800-80040600	Weak transcription	Spleen	Spleen
46	chr5:80022800-80041400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:80022800-80051200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:80023000-80030800	Weak transcription	Fetal Intestine Small	intestine
49	chr5:80023000-80031200	Weak transcription	Fetal Stomach	stomach
50	chr5:80023000-80032400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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