Variant report

Variant	rs17369104
Chromosome Location	chr5:107144755-107144756
allele	A/G
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	USF2	chr5:107144255-107144797	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr5:107144387-107144928	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr5:107144393-107144818	ECC-1	luminal epithelium:	n/a	n/a
4	USF1	chr5:107144425-107144877	H1-hESC	embryonic stem cell:	n/a	n/a
5	NANOG	chr5:107144489-107144851	H1-hESC	embryonic stem cell:	n/a	chr5:107144664-107144673
6	YY1	chr5:107144418-107144817	ECC-1	luminal epithelium:	n/a	n/a
7	SP1	chr5:107144340-107145209	H1-hESC	embryonic stem cell:	n/a	chr5:107144692-107144701 chr5:107144691-107144703 chr5:107144693-107144702 chr5:107144692-107144702
8	TEAD4	chr5:107144401-107144795	ECC-1	luminal epithelium:	n/a	n/a
9	USF1	chr5:107144423-107144841	H1-hESC	embryonic stem cell:	n/a	n/a
10	TCF12	chr5:107144566-107144867	H1-hESC	embryonic stem cell:	n/a	n/a
11	ZNF263	chr5:107144182-107144876	HEK293-T-REx	kidney:	n/a	chr5:107144495-107144504 chr5:107144492-107144501
12	HDAC2	chr5:107144386-107145282	H1-hESC	embryonic stem cell:	n/a	chr5:107144961-107144975 chr5:107144966-107144980 chr5:107144969-107144983
13	CTBP2	chr5:107144294-107145213	H1-hESC	embryonic stem cell:	n/a	n/a
14	HDAC2	chr5:107144529-107144879	H1-hESC	embryonic stem cell:	n/a	n/a
15	TEAD4	chr5:107144473-107144843	H1-hESC	embryonic stem cell:	n/a	n/a
16	KAP1	chr5:107144210-107144846	HEK293	kidney:	n/a	n/a
17	KAP1	chr5:107144247-107144830	U2OS	brain:	n/a	n/a
18	SIN3A	chr5:107144304-107145029	H1-hESC	embryonic stem cell:	n/a	chr5:107144324-107144334 chr5:107144655-107144668
19	MXI1	chr5:107144327-107144819	H1-hESC	embryonic stem cell:	n/a	chr5:107144644-107144653
20	USF1	chr5:107144444-107144904	ECC-1	luminal epithelium:	n/a	n/a
21	TCF12	chr5:107144481-107144901	H1-hESC	embryonic stem cell:	n/a	n/a
22	SP4	chr5:107144425-107144838	H1-hESC	embryonic stem cell:	n/a	chr5:107144689-107144705
23	EP300	chr5:107144404-107144896	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RN7SKP122	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10515380	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253	0.86[CEU][hapmap]
rs12186563	0.87[ASN][1000 genomes]
rs12187616	0.87[ASN][1000 genomes]
rs12188414	0.85[CEU][hapmap]
rs12189428	0.86[CEU][hapmap];1.00[MEX][hapmap]
rs12513976	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519254	0.86[CEU][hapmap];1.00[MEX][hapmap]
rs12519388	0.86[CEU][hapmap]
rs12520230	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12522548	0.86[CEU][hapmap];1.00[MEX][hapmap]
rs12522552	0.86[CEU][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap]
rs17160706	0.90[MEX][hapmap]
rs17435188	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3842914	0.82[ASN][1000 genomes]
rs3842915	0.82[ASN][1000 genomes]
rs3843491	0.82[ASN][1000 genomes]
rs3843492	0.82[ASN][1000 genomes]
rs62355954	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355956	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864994	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7736608	0.82[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	nsv830440	chr5:107074116-107278905	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1022155	chr5:107138981-107149604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17369104	SLC25A46	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107138400-107144800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:107140400-107148800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:107140800-107145000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr5:107140800-107146600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:107141400-107146000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:107141400-107146600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:107142400-107144800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:107142400-107145200	Weak transcription	Hela-S3	cervix
9	chr5:107142600-107145400	Enhancers	Fetal Kidney	kidney
10	chr5:107142800-107145000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:107142800-107145000	Weak transcription	NHLF	lung
12	chr5:107143000-107148000	Weak transcription	HSMM	muscle
13	chr5:107143600-107145800	Weak transcription	Fetal Heart	heart
14	chr5:107143600-107148000	Weak transcription	HSMMtube	muscle
15	chr5:107143800-107145800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr5:107144000-107144800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:107144000-107144800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:107144000-107144800	Enhancers	Fetal Intestine Small	intestine
19	chr5:107144000-107144800	Enhancers	Fetal Muscle Leg	muscle
20	chr5:107144000-107144800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr5:107144000-107145200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:107144000-107145800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr5:107144000-107145800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr5:107144000-107146200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:107144000-107146600	Enhancers	H9 Cell Line	embryonic stem cell
26	chr5:107144200-107144800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:107144200-107144800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr5:107144200-107144800	Enhancers	Right Atrium	heart
29	chr5:107144200-107145000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr5:107144200-107145200	Enhancers	Fetal Thymus	thymus
31	chr5:107144200-107145600	Enhancers	Fetal Stomach	stomach
32	chr5:107144200-107145800	Enhancers	NH-A	brain
33	chr5:107144400-107144800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:107144400-107144800	Enhancers	Brain Germinal Matrix	brain
35	chr5:107144400-107144800	Enhancers	Dnd41	blood
36	chr5:107144400-107145000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:107144400-107145600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:107144400-107146200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:107144400-107167600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:107144600-107144800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr5:107144600-107144800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr5:107144600-107144800	Enhancers	Esophagus	oesophagus
43	chr5:107144600-107145000	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr5:107144600-107145400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr5:107144600-107145600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:107144600-107145800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:107144600-107145800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links