Variant report

Variant	rs4703827
Chromosome Location	chr5:80528135-80528136
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:80527695-80529481	HepG2	liver:	n/a	n/a
2	MAX	chr5:80528103-80528650	ECC-1	luminal epithelium:	n/a	chr5:80528405-80528415 chr5:80528404-80528415 chr5:80528405-80528415 chr5:80528185-80528200 chr5:80528403-80528416

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACOT12-8	chr5:80521955-80529138	NONHSAT102436
2	lnc-ACOT12-8	chr5:80528125-80529661	NONHSAT102437

Variant related genes	Relation type
CKMT2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10036376	0.81[CEU][hapmap]
rs10038684	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10041063	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053706	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10055063	0.82[EUR][1000 genomes]
rs10066296	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10078279	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10474656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514215	0.81[CEU][hapmap]
rs1055383	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10942945	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950033	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13362314	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1566432	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294418	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17294956	0.81[CEU][hapmap]
rs2270823	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28464111	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650401	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897389	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704707	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704708	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704710	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704712	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704715	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704720	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59132806	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60488995	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60904680	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61244991	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866499	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap]
rs6893467	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73130869	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381116	0.84[AMR][1000 genomes]
rs7448717	0.94[CEU][hapmap]
rs750728	0.81[CEU][hapmap]
rs7709071	1.00[CHB][hapmap]
rs7709149	1.00[CHB][hapmap]
rs7720009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7728465	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734902	1.00[CHB][hapmap]
rs921928	1.00[CHB][hapmap]
rs9293841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4703827	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs4703827	CTC-281B15.1	cis	Stomach	GTEx
rs4703827	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs4703827	CTC-281B15.1	cis	Thyroid	GTEx
rs4703827	CTD-2248H3.1	cis	lung	GTEx
rs4703827	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs4703827	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs4703827	BHMT2	cis	cerebellum	SCAN
rs4703827	CKMT2	cis	normal skin	skin_eQTL
rs4703827	CTC-281B15.1	cis	Artery Aorta	GTEx
rs4703827	CTD-2248H3.1	cis	Thyroid	GTEx
rs4703827	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs4703827	CTC-281B15.1	cis	lung	GTEx
rs4703827	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80464200-80528400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:80465200-80528200	Weak transcription	Ovary	ovary
3	chr5:80491000-80528400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:80491200-80530000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:80491400-80528400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:80492000-80528600	Weak transcription	Left Ventricle	heart
7	chr5:80498000-80528800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:80498800-80530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:80506000-80530000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:80507600-80528200	Weak transcription	HepG2	liver
11	chr5:80509000-80528400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:80509200-80528800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:80509400-80530000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:80510600-80528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:80516400-80528600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:80520600-80530200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:80521000-80528600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:80522400-80530000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:80522600-80528800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:80522600-80530400	Weak transcription	Primary T cells from cord blood	blood
21	chr5:80522800-80528200	Weak transcription	Adipose Nuclei	Adipose
22	chr5:80523200-80528800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:80524200-80528200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:80524200-80528400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr5:80525800-80528200	Weak transcription	Brain Angular Gyrus	brain
26	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:80527000-80528600	Enhancers	Fetal Muscle Leg	muscle
29	chr5:80527000-80530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:80527200-80528200	Enhancers	Fetal Heart	heart
32	chr5:80527200-80528200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr5:80527200-80528600	Enhancers	HSMMtube	muscle
34	chr5:80527400-80528400	Enhancers	Fetal Muscle Trunk	muscle
35	chr5:80527400-80528600	Enhancers	Brain Substantia Nigra	brain
36	chr5:80527800-80528200	Enhancers	Brain Hippocampus Middle	brain
37	chr5:80527800-80528200	Enhancers	Stomach Smooth Muscle	stomach
38	chr5:80527800-80528400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:80527800-80529400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr5:80528000-80528400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:80528000-80528400	Enhancers	Brain Cingulate Gyrus	brain
42	chr5:80528000-80528400	Enhancers	Colon Smooth Muscle	Colon
43	chr5:80528000-80528400	Enhancers	Rectal Smooth Muscle	rectum
44	chr5:80528000-80528600	Enhancers	NHDF-Ad	bronchial
45	chr5:80528000-80528600	Enhancers	NHLF	lung
46	chr5:80528000-80528800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr5:80528000-80529200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix

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