Variant report

Variant	rs62156346
Chromosome Location	chr2:98991264-98991265
allele	C/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	FOXA1	chr2:98991010-98991284	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98965022..98967401-chr2:98990088..98992625,2	MCF-7	breast:

Variant related genes	Relation type
CNGA3	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1010387	1.00[AFR][1000 genomes]
rs11684812	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11684899	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691306	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17427608	1.00[AFR][1000 genomes]
rs17427825	1.00[AFR][1000 genomes]
rs17428990	1.00[AFR][1000 genomes]
rs17501094	1.00[AFR][1000 genomes]
rs62155312	1.00[AFR][1000 genomes]
rs62155317	1.00[AFR][1000 genomes]
rs62155347	1.00[AFR][1000 genomes]
rs62155355	1.00[AFR][1000 genomes]
rs62155358	1.00[AFR][1000 genomes]
rs62156265	1.00[AFR][1000 genomes]
rs62156266	1.00[AFR][1000 genomes]
rs62156268	1.00[AFR][1000 genomes]
rs62156269	1.00[AFR][1000 genomes]
rs62156305	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62156686	1.00[AFR][1000 genomes]
rs62156724	1.00[AFR][1000 genomes]
rs62156744	1.00[AFR][1000 genomes]
rs62157892	1.00[AFR][1000 genomes]
rs62157901	1.00[AFR][1000 genomes]
rs62157907	1.00[AFR][1000 genomes]
rs62157908	1.00[AFR][1000 genomes]
rs72817785	1.00[AFR][1000 genomes]
rs72817792	1.00[AFR][1000 genomes]
rs72817793	1.00[AFR][1000 genomes]
rs72819903	1.00[AFR][1000 genomes]
rs72819919	1.00[AFR][1000 genomes]
rs72819925	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98979200-98991400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:98983200-98993400	Weak transcription	Fetal Brain Female	brain
3	chr2:98985200-98991800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:98986000-98992800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:98989200-98994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:98989600-98992600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:98989800-98992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:98990600-98991800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:98990600-99007200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:98991000-98991400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:98991000-98992800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:98991000-98994600	Weak transcription	Ovary	ovary
13	chr2:98991200-98992600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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