Variant report

Variant	rs245407
Chromosome Location	chr5:80096734-80096735
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:80087165..80090080-chr5:80096235..80098105,2	K562	blood:
2	chr5:80090734..80092414-chr5:80095592..80098370,2	K562	blood:
3	chr5:80092334..80094934-chr5:80095470..80097531,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1679115	0.89[EUR][1000 genomes]
rs168653	0.87[EUR][1000 genomes]
rs245340	0.86[EUR][1000 genomes]
rs245341	0.86[EUR][1000 genomes]
rs245348	0.87[EUR][1000 genomes]
rs245355	0.87[EUR][1000 genomes]
rs245356	0.87[EUR][1000 genomes]
rs245357	0.87[EUR][1000 genomes]
rs245360	0.87[EUR][1000 genomes]
rs245372	0.85[EUR][1000 genomes]
rs245373	0.87[EUR][1000 genomes]
rs245374	0.87[EUR][1000 genomes]
rs245379	0.86[EUR][1000 genomes]
rs245380	0.87[EUR][1000 genomes]
rs245385	0.87[EUR][1000 genomes]
rs245386	0.86[EUR][1000 genomes]
rs245389	0.88[EUR][1000 genomes]
rs26278	0.87[EUR][1000 genomes]
rs26279	0.85[EUR][1000 genomes]
rs27366	0.87[EUR][1000 genomes]
rs27494	0.86[EUR][1000 genomes]
rs27887	0.86[EUR][1000 genomes]
rs32963	0.86[EUR][1000 genomes]
rs32964	0.86[EUR][1000 genomes]
rs32967	0.86[EUR][1000 genomes]
rs32968	0.86[EUR][1000 genomes]
rs32988	0.89[EUR][1000 genomes]
rs32989	0.89[EUR][1000 genomes]
rs32999	0.86[EUR][1000 genomes]
rs39626	0.88[EUR][1000 genomes]
rs40591	0.89[EUR][1000 genomes]
rs9293824	0.80[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs245407	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs245407	MSH3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 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	chr5:79985000-80100600	Weak transcription	Brain Germinal Matrix	brain
3	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:80041200-80100400	Weak transcription	Gastric	stomach
5	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
6	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
7	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
9	chr5:80076200-80109600	Weak transcription	HepG2	liver
10	chr5:80077400-80108000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:80077600-80112000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:80083000-80101400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr5:80083200-80098400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr5:80083800-80098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:80088200-80109600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:80089400-80110400	Weak transcription	Hela-S3	cervix
21	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:80089600-80100000	Weak transcription	HMEC	breast
24	chr5:80089600-80109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:80089600-80110200	Weak transcription	Brain Angular Gyrus	brain
26	chr5:80089600-80118400	Weak transcription	NHEK	skin
27	chr5:80089800-80112400	Weak transcription	K562	blood
28	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:80090000-80109400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:80090000-80111000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:80090200-80109200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:80090400-80098200	Weak transcription	Fetal Kidney	kidney
35	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:80090600-80109400	Weak transcription	HSMMtube	muscle
37	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr5:80090800-80097000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:80091000-80096800	Weak transcription	Aorta	Aorta
40	chr5:80091000-80103400	Weak transcription	Ovary	ovary
41	chr5:80091000-80109200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:80091000-80109200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr5:80091000-80109400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:80091000-80116600	Weak transcription	A549	lung
45	chr5:80091200-80109000	Weak transcription	HSMM	muscle
46	chr5:80091200-80109200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:80091200-80110600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr5:80091200-80116000	Weak transcription	Brain Substantia Nigra	brain
49	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr5:80091400-80096800	Weak transcription	Primary hematopoietic stem cells	blood

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