Variant report

Variant	rs33008
Chromosome Location	chr5:80078581-80078582
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:80040441..80042841-chr5:80078173..80081094,2	K562	blood:
2	chr5:80067813..80069872-chr5:80077302..80079329,2	K562	blood:
3	chr5:80067813..80071581-chr5:80076574..80078808,3	K562	blood:
4	chr5:80074238..80076204-chr5:80077770..80080634,2	K562	blood:

Variant related genes	Relation type
ENSG00000248967	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs151886	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs245009	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs245014	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs245336	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs245390	0.80[EUR][1000 genomes]
rs245391	0.80[EUR][1000 genomes]
rs245392	1.00[CEU][hapmap];0.87[YRI][hapmap];0.80[EUR][1000 genomes]
rs245393	0.82[EUR][1000 genomes]
rs245398	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs245404	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs26780	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs26781	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs26782	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28059	0.92[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32951	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs32953	0.81[EUR][1000 genomes]
rs32960	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33011	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776972	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40592	0.87[EUR][1000 genomes]
rs41097	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6151627	0.92[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap]
rs6151629	0.95[CEU][hapmap];0.93[YRI][hapmap]
rs6151653	0.92[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap]
rs6151670	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap]
rs6151706	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6151707	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7712332	0.86[CHD][hapmap]
rs857288	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs33008	MSH3	cis	multi-tissue	Pritchard
rs33008	DHFR	cis	Muscle Skeletal	GTEx
rs33008	JMY	cis	parietal	SCAN

Chromatin state (count:108 , 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	chr5:80041800-80094200	Weak transcription	NHLF	lung
6	chr5:80042800-80089200	Weak transcription	Brain Substantia Nigra	brain
7	chr5:80042800-80118200	Weak transcription	Spleen	Spleen
8	chr5:80042800-80173400	Weak transcription	Right Ventricle	heart
9	chr5:80043600-80089000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr5:80044000-80096400	Weak transcription	Brain Anterior Caudate	brain
11	chr5:80048800-80088000	Weak transcription	Fetal Kidney	kidney
12	chr5:80049400-80089000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:80049800-80088800	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:80051000-80078600	Weak transcription	NHDF-Ad	bronchial
15	chr5:80051200-80084000	Weak transcription	Thymus	Thymus
16	chr5:80051600-80088600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:80051600-80088800	Weak transcription	Colonic Mucosa	Colon
18	chr5:80051600-80095000	Weak transcription	Psoas Muscle	Psoas
19	chr5:80051800-80089000	Weak transcription	HSMMtube	muscle
20	chr5:80052200-80095600	Weak transcription	Fetal Brain Male	brain
21	chr5:80052400-80085400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:80053000-80088600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:80056800-80089000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:80057000-80085600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:80057200-80083800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:80057200-80088000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:80057200-80090000	Weak transcription	Aorta	Aorta
28	chr5:80057200-80094200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:80057400-80089200	Weak transcription	K562	blood
30	chr5:80058000-80089000	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:80059400-80088600	Weak transcription	Fetal Brain Female	brain
32	chr5:80059600-80089200	Weak transcription	Lung	lung
33	chr5:80059800-80085400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr5:80064400-80088600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:80064600-80088800	Weak transcription	HSMM	muscle
36	chr5:80064800-80089200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr5:80069000-80093600	Weak transcription	Pancreas	Pancrea
38	chr5:80069400-80089200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:80070200-80086000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:80072000-80079600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr5:80072200-80081200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr5:80072800-80089000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:80073200-80093600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:80073400-80112800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:80073600-80089200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:80073600-80089600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr5:80073800-80089000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:80074000-80086400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr5:80074000-80088000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:80074000-80088600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links