Variant report

Variant	rs10209575
Chromosome Location	chr2:233557990-233557991
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	SETDB1	chr2:233557960-233558526	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:233557000..233560221-chr2:233560473..233563439,3	MCF-7	breast:
2	chr2:233551304..233553679-chr2:233557579..233559431,2	MCF-7	breast:
3	chr2:233556555..233559302-chr2:233560158..233563779,3	MCF-7	breast:

Variant related genes	Relation type
GIGYF2	TF binding region
ENSG00000204120	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10190211	0.90[EUR][1000 genomes]
rs10933407	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10933408	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11679581	0.86[EUR][1000 genomes]
rs11685169	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11687379	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11688622	0.88[EUR][1000 genomes]
rs11688691	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11694434	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11695762	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12052869	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12694915	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12694916	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13386650	0.95[EUR][1000 genomes]
rs13396293	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13412034	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13412513	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13425525	0.89[EUR][1000 genomes]
rs13429857	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1446307	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2289914	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2289915	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2293782	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2305139	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs34063802	0.92[EUR][1000 genomes]
rs34832091	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35778045	0.92[EUR][1000 genomes]
rs35785837	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35928329	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41266951	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs56054779	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62193305	0.86[EUR][1000 genomes]
rs6747479	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73005582	0.86[EUR][1000 genomes]
rs7557131	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7564554	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9288675	0.95[EUR][1000 genomes]
rs9288676	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9808146	0.86[EUR][1000 genomes]
rs9973586	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10209575	C2orf82	cis	brain	BrainEAC
rs10209575	C2orf82	cis	frontal cortex	BrainEAC

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233538200-233561400	Weak transcription	Right Ventricle	heart
2	chr2:233546800-233561400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:233547400-233560600	Weak transcription	Placenta	Placenta
4	chr2:233547400-233561200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:233547800-233561400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:233548600-233561600	Weak transcription	Aorta	Aorta
7	chr2:233549200-233561200	Weak transcription	Brain Substantia Nigra	brain
8	chr2:233553000-233561200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:233554600-233561400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:233554800-233561200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:233555000-233561400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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