Variant report

Variant	rs1644201
Chromosome Location	chr5:80112002-80112003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs245338	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs245343	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs245345	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs245346	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs245351	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs245362	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs245378	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs32982	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs32991	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32993	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33002	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1644201	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs1644201	DHFR	cis	Adipose Subcutaneous	GTEx
rs1644201	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs1644201	DHFR	cis	Muscle Skeletal	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79971800-80112400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
3	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
4	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
6	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:80089600-80118400	Weak transcription	NHEK	skin
13	chr5:80089800-80112400	Weak transcription	K562	blood
14	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr5:80091000-80116600	Weak transcription	A549	lung
20	chr5:80091200-80116000	Weak transcription	Brain Substantia Nigra	brain
21	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:80091400-80114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:80091400-80114800	Weak transcription	Thymus	Thymus
24	chr5:80091400-80117600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:80091400-80118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:80091400-80124600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:80091400-80124600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr5:80091400-80124600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:80091400-80181000	Weak transcription	Small Intestine	intestine
30	chr5:80091800-80125200	Weak transcription	Osteobl	bone
31	chr5:80093000-80124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:80093800-80123800	Weak transcription	Pancreas	Pancrea
33	chr5:80094800-80124000	Weak transcription	GM12878-XiMat	blood
34	chr5:80095000-80113000	Weak transcription	Lung	lung
35	chr5:80095200-80115400	Weak transcription	Psoas Muscle	Psoas
36	chr5:80095200-80116600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:80096600-80118400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:80097000-80124400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:80097600-80121400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:80097600-80121600	Weak transcription	Brain Hippocampus Middle	brain
41	chr5:80097800-80121600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr5:80098400-80121600	Weak transcription	Brain Anterior Caudate	brain
43	chr5:80099200-80117200	Weak transcription	Fetal Brain Male	brain
44	chr5:80099200-80121400	Weak transcription	Fetal Lung	lung
45	chr5:80100400-80118400	Weak transcription	HMEC	breast
46	chr5:80103000-80118400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:80103800-80118400	Weak transcription	Ovary	ovary
48	chr5:80103800-80144600	Weak transcription	Gastric	stomach
49	chr5:80106400-80119400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:80106600-80112200	Weak transcription	Fetal Kidney	kidney

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