Variant report

Variant	rs32998
Chromosome Location	chr5:80107257-80107258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10041898	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10057510	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs184967	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245337	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245339	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245344	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245347	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245350	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs245352	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245353	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245354	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245358	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs245359	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245361	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245366	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245368	0.81[AMR][1000 genomes]
rs245369	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245370	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs245371	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs245375	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245381	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245382	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs245383	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245384	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs245387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs245394	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs245395	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs245396	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs245397	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245403	0.82[EUR][1000 genomes]
rs245408	0.80[EUR][1000 genomes]
rs32965	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs32966	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs32980	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs32984	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs32987	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs32994	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33001	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs33009	0.86[EUR][1000 genomes]
rs33010	0.86[EUR][1000 genomes]
rs33012	0.86[EUR][1000 genomes]
rs35039937	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs39627	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs39628	0.82[EUR][1000 genomes]
rs40408	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41100	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs42290	0.86[EUR][1000 genomes]
rs6869090	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6870306	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71636249	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71636250	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71636251	0.82[AMR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs32998	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 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	chr5:79998800-80109400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
4	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
5	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr5:80075200-80114000	Weak transcription	Stomach Mucosa	stomach
7	chr5:80076200-80109600	Weak transcription	HepG2	liver
8	chr5:80077400-80108000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:80077600-80112000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:80077600-80118800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:80085200-80127600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:80087400-80132800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:80087800-80167400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:80088200-80109600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:80089400-80110400	Weak transcription	Hela-S3	cervix
16	chr5:80089400-80118400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:80089400-80120200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:80089600-80109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:80089600-80110200	Weak transcription	Brain Angular Gyrus	brain
20	chr5:80089600-80118400	Weak transcription	NHEK	skin
21	chr5:80089800-80112400	Weak transcription	K562	blood
22	chr5:80089800-80118400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:80090000-80109400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:80090000-80111000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:80090000-80118600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:80090200-80109200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:80090200-80118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr5:80090400-80124600	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:80090600-80109400	Weak transcription	HSMMtube	muscle
30	chr5:80090600-80124000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:80091000-80109200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:80091000-80109200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:80091000-80109400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:80091000-80116600	Weak transcription	A549	lung
35	chr5:80091200-80109000	Weak transcription	HSMM	muscle
36	chr5:80091200-80109200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:80091200-80110600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:80091200-80116000	Weak transcription	Brain Substantia Nigra	brain
39	chr5:80091200-80144400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:80091400-80109200	Weak transcription	Placenta	Placenta
41	chr5:80091400-80109200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:80091400-80109400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:80091400-80109400	Weak transcription	Fetal Thymus	thymus
44	chr5:80091400-80114200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:80091400-80114800	Weak transcription	Thymus	Thymus
46	chr5:80091400-80117600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:80091400-80118600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:80091400-80124600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:80091400-80124600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr5:80091400-80124600	Weak transcription	Rectal Smooth Muscle	rectum

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