Variant report

Variant	rs1870061
Chromosome Location	chr5:80528457-80528458
allele	G/T
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	chr5:80528326-80528515	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:80528433-80528594	HepG2	liver:	n/a	n/a
3	HEY1	chr5:80528306-80528634	HepG2	liver:	n/a	n/a
4	REST	chr5:80528393-80528752	ECC-1	luminal epithelium:	n/a	chr5:80528476-80528485 chr5:80528476-80528496 chr5:80528733-80528746
5	USF1	chr5:80528268-80528631	ECC-1	luminal epithelium:	n/a	chr5:80528404-80528415
6	POLR2A	chr5:80528322-80529449	HepG2	liver:	n/a	n/a
7	NFIC	chr5:80528257-80529399	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr5:80527695-80529481	HepG2	liver:	n/a	n/a
9	CHD2	chr5:80528366-80528459	HepG2	liver:	n/a	n/a
10	REST	chr5:80528365-80528583	K562	blood:	n/a	chr5:80528476-80528485 chr5:80528476-80528496
11	USF1	chr5:80528286-80528520	HepG2	liver:	n/a	chr5:80528404-80528415
12	POLR2A	chr5:80528324-80528763	K562	blood:	n/a	n/a
13	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
14	BHLHE40	chr5:80528359-80528491	K562	blood:	n/a	n/a
15	NFIC	chr5:80528244-80528773	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr5:80528284-80528588	HepG2	liver:	n/a	chr5:80528405-80528415 chr5:80528404-80528415 chr5:80528405-80528415 chr5:80528403-80528416
17	REST	chr5:80528328-80528630	ECC-1	luminal epithelium:	n/a	chr5:80528476-80528485 chr5:80528476-80528496
18	FOSL2	chr5:80528259-80529498	HepG2	liver:	n/a	chr5:80529093-80529102
19	REST	chr5:80528369-80528598	H1-hESC	embryonic stem cell:	n/a	chr5:80528476-80528485 chr5:80528476-80528496
20	POLR2A	chr5:80528304-80528541	HepG2	liver:	n/a	n/a
21	POLR2A	chr5:80528360-80528591	HepG2	liver:	n/a	n/a
22	POLR2A	chr5:80528373-80529376	HepG2	liver:	n/a	n/a
23	RFX5	chr5:80528317-80528514	HepG2	liver:	n/a	n/a
24	MAX	chr5:80528232-80528573	K562	blood:	n/a	chr5:80528405-80528415 chr5:80528404-80528415 chr5:80528405-80528415 chr5:80528403-80528416
25	POLR2A	chr5:80528286-80528621	HepG2	liver:	n/a	n/a
26	REST	chr5:80528366-80528560	H1-hESC	embryonic stem cell:	n/a	chr5:80528476-80528485 chr5:80528476-80528496
27	MAX	chr5:80528181-80528688	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: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10073527	1.00[JPT][hapmap]
rs12652649	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13155580	1.00[JPT][hapmap]
rs13159978	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34755999	0.86[AMR][1000 genomes]
rs545	1.00[JPT][hapmap]
rs59563495	0.89[EUR][1000 genomes]
rs6872504	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80491200-80530000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:80492000-80528600	Weak transcription	Left Ventricle	heart
3	chr5:80498000-80528800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:80498800-80530000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:80506000-80530000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:80509200-80528800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:80509400-80530000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:80510600-80528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:80516400-80528600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:80520600-80530200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr5:80521000-80528600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:80522400-80530000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:80522600-80528800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:80522600-80530400	Weak transcription	Primary T cells from cord blood	blood
15	chr5:80523200-80528800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:80527000-80528600	Enhancers	Fetal Muscle Leg	muscle
19	chr5:80527000-80530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:80527200-80528600	Enhancers	HSMMtube	muscle
22	chr5:80527400-80528600	Enhancers	Brain Substantia Nigra	brain
23	chr5:80527800-80529400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr5:80528000-80528600	Enhancers	NHDF-Ad	bronchial
25	chr5:80528000-80528600	Enhancers	NHLF	lung
26	chr5:80528000-80528800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr5:80528000-80529200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
29	chr5:80528200-80528600	Enhancers	Ovary	ovary
30	chr5:80528200-80529000	Flanking Active TSS	Fetal Heart	heart
31	chr5:80528200-80529400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr5:80528200-80529400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr5:80528200-80529600	Enhancers	Fetal Lung	lung
34	chr5:80528200-80531000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:80528200-80531800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr5:80528400-80528600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:80528400-80528600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr5:80528400-80528600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr5:80528400-80528600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr5:80528400-80528600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr5:80528400-80528600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:80528400-80528600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr5:80528400-80528600	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr5:80528400-80528600	Active TSS	Brain Angular Gyrus	brain
45	chr5:80528400-80528600	Flanking Active TSS	Brain Cingulate Gyrus	brain
46	chr5:80528400-80528600	Enhancers	Fetal Stomach	stomach
47	chr5:80528400-80528600	Enhancers	Right Ventricle	heart
48	chr5:80528400-80528800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr5:80528400-80528800	Enhancers	H9 Cell Line	embryonic stem cell
50	chr5:80528400-80528800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links