Variant report

Variant	rs11852448
Chromosome Location	chr15:59888063-59888064
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	HNF4A	chr15:59887653-59888149	HepG2	liver:	n/a	chr15:59887837-59887845 chr15:59887831-59887843 chr15:59887956-59887964 chr15:59887836-59887844 chr15:59887766-59887778 chr15:59887829-59887844 chr15:59887838-59887846
2	JUND	chr15:59887675-59888090	HepG2	liver:	n/a	n/a
3	TCF12	chr15:59886353-59888398	A549	lung:	n/a	chr15:59887089-59887099
4	HDAC2	chr15:59887614-59888092	HepG2	liver:	n/a	chr15:59887836-59887844
5	FOXA1	chr15:59887648-59888101	HepG2	liver:	n/a	n/a
6	FOXA1	chr15:59887770-59888098	HepG2	liver:	n/a	n/a
7	ELF1	chr15:59887572-59888113	HepG2	liver:	n/a	n/a
8	MAZ	chr15:59887860-59888224	HepG2	liver:	n/a	n/a
9	MAX	chr15:59887486-59888188	A549	lung:	n/a	n/a
10	MAX	chr15:59886489-59888320	A549	lung:	n/a	chr15:59886710-59886719
11	ELF1	chr15:59887587-59888159	HepG2	liver:	n/a	n/a
12	FOXA2	chr15:59887745-59888126	HepG2	liver:	n/a	n/a
13	EP300	chr15:59887585-59888164	HepG2	liver:	n/a	n/a
14	TEAD4	chr15:59887422-59888164	HepG2	liver:	n/a	n/a
15	EP300	chr15:59886370-59888218	A549	lung:	n/a	n/a
16	SP1	chr15:59886467-59888083	A549	lung:	n/a	n/a
17	EP300	chr15:59886471-59888087	A549	lung:	n/a	n/a
18	FOXA1	chr15:59887717-59888150	HepG2	liver:	n/a	n/a
19	SP1	chr15:59886313-59888215	A549	lung:	n/a	n/a
20	GATA3	chr15:59886400-59888118	A549	lung:	n/a	chr15:59886709-59886718
21	POLR2A	chr15:59887916-59888068	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GCNT3-2	chr15:59887928-59888112	NONHSAT044179

Variant related genes	Relation type
GCNT3	TF binding region

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10163153	0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs11071458	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11852458	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11852547	0.86[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs12438840	0.82[EUR][1000 genomes]
rs12440292	0.86[CHB][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs12901058	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1552033	0.90[CHB][hapmap];0.88[EUR][1000 genomes]
rs1552034	0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs17269684	0.82[CHB][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs34444281	0.82[EUR][1000 genomes]
rs34642067	0.83[EUR][1000 genomes]
rs4597252	0.81[EUR][1000 genomes]
rs71480535	0.82[EUR][1000 genomes]
rs7169937	0.89[CHB][hapmap]
rs7171752	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8036403	0.82[CHB][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs8037054	0.90[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv569606	chr15:59883809-59894636	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11852448	TCF12	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59882400-59891600	Weak transcription	Small Intestine	intestine
2	chr15:59886000-59889400	Enhancers	Fetal Intestine Small	intestine
3	chr15:59886400-59888200	Enhancers	Osteobl	bone
4	chr15:59886400-59888600	Flanking Active TSS	A549	lung
5	chr15:59886600-59888200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:59886600-59889400	Enhancers	Stomach Mucosa	stomach
7	chr15:59886800-59888200	Flanking Active TSS	HepG2	liver
8	chr15:59886800-59888600	Enhancers	Ovary	ovary
9	chr15:59886800-59888800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:59886800-59892800	Enhancers	Fetal Intestine Large	intestine
11	chr15:59887400-59889400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr15:59887800-59888200	Weak transcription	Gastric	stomach
13	chr15:59887800-59888200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr15:59887800-59889800	Enhancers	Colonic Mucosa	Colon
15	chr15:59888000-59888200	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr15:59888000-59888800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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