Variant report

Variant	rs7159300
Chromosome Location	chr14:72883874-72883875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr14:72883681-72883920	GM12878	blood:	n/a	n/a
2	CTCF	chr14:72883367-72884088	MCF-7	breast:	n/a	n/a
3	CTCF	chr14:72883650-72883885	GM12891	blood:	n/a	n/a
4	CTCF	chr14:72883629-72883905	MCF-7	breast:	n/a	n/a
5	RAD21	chr14:72883601-72883895	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr14:72883760-72883910	GM12878	blood:	n/a	n/a
7	ARID3A	chr14:72883805-72883894	HepG2	liver:	n/a	n/a
8	CTCF	chr14:72883453-72884058	MCF-7	breast:	n/a	n/a
9	CTCF	chr14:72883641-72883905	MCF-7	breast:	n/a	n/a
10	RAD21	chr14:72883481-72884058	MCF-7	breast:	n/a	n/a
11	RAD21	chr14:72883504-72883888	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr14:72883632-72883897	GM12892	blood:	n/a	n/a
13	CTCF	chr14:72883621-72883901	MCF-7	breast:	n/a	n/a
14	CTCF	chr14:72883668-72883878	A549	lung:	n/a	n/a
15	RAD21	chr14:72883620-72883883	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr14:72883606-72883925	GM12878	blood:	n/a	n/a
17	RAD21	chr14:72883389-72884059	MCF-7	breast:	n/a	n/a
18	CTCF	chr14:72883760-72883910	GM12866	blood:	n/a	n/a
19	SMC3	chr14:72883636-72883901	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr14:72883645-72883908	LNCaP	prostate:	n/a	n/a
21	CTCF	chr14:72883626-72883907	MCF-7	breast:	n/a	n/a
22	CTCF	chr14:72883575-72883963	GM12878	blood:	n/a	n/a
23	CTCF	chr14:72883622-72883908	MCF-7	breast:	n/a	n/a
24	CTCF	chr14:72883617-72883886	LNCaP	prostate:	n/a	n/a
25	CTCF	chr14:72883663-72883892	GM19240	blood:	n/a	n/a
26	ZNF143	chr14:72883596-72883896	H1-hESC	embryonic stem cell:	n/a	n/a
27	PAX5	chr14:72883611-72883876	GM12878	blood:	n/a	chr14:72883774-72883793
28	EBF1	chr14:72883694-72883951	GM12878	blood:	n/a	n/a
29	MYC	chr14:72883646-72883902	MCF-7	breast:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72760434..72761186-chr14:72883286..72884169,5	MCF-7	breast:

No data

Variant related genes	Relation type
RGS6	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10134133	0.89[EUR][1000 genomes]
rs10144932	0.89[EUR][1000 genomes]
rs11158954	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs12434786	0.81[TSI][hapmap]
rs12435911	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239216	0.96[CHD][hapmap];0.86[GIH][hapmap];0.86[ASN][1000 genomes]
rs6574073	0.96[CHD][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6574076	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7151688	0.87[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8015756	0.83[TSI][hapmap]

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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Smoking cessation	20811658	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7159300	PCNX	cis	parietal	SCAN
rs7159300	TMED10	cis	parietal	SCAN
rs7159300	MLH3	cis	cerebellum	SCAN
rs7159300	C14orf43	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72882600-72885200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr14:72882800-72885600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr14:72883200-72884000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:72883400-72884000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr14:72883600-72884200	Enhancers	Left Ventricle	heart
6	chr14:72883800-72884400	Enhancers	Fetal Brain Male	brain
7	chr14:72883800-72884600	Enhancers	Fetal Brain Female	brain
8	chr14:72883800-72884800	Enhancers	Placenta	Placenta

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