Variant report

Variant	rs35189503
Chromosome Location	chr2:55725641-55725642
allele	A/T
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	GATA3	chr2:55725240-55725849	SK-N-SH	brain:	n/a	chr2:55725506-55725522
2	GATA3	chr2:55725267-55725757	SK-N-SH	brain:	n/a	chr2:55725506-55725522

Variant related genes	Relation type
RNU6-634P	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12612227	0.83[EUR][1000 genomes]
rs12618859	0.85[EUR][1000 genomes]
rs12986587	0.97[ASN][1000 genomes]
rs12986797	0.85[EUR][1000 genomes]
rs12987272	0.87[AMR][1000 genomes]
rs12992827	0.96[ASN][1000 genomes]
rs12993642	0.96[ASN][1000 genomes]
rs12994656	0.80[AMR][1000 genomes]
rs12998664	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13005678	0.80[ASN][1000 genomes]
rs13009906	0.80[ASN][1000 genomes]
rs13019595	0.86[EUR][1000 genomes]
rs13022396	0.96[ASN][1000 genomes]
rs13025994	0.80[AMR][1000 genomes]
rs13030396	0.80[AMR][1000 genomes]
rs13032503	0.81[ASN][1000 genomes]
rs17737233	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1867334	0.85[AMR][1000 genomes]
rs2054729	0.80[AMR][1000 genomes]
rs2291336	0.84[EUR][1000 genomes]
rs34129478	0.85[EUR][1000 genomes]
rs34400247	0.82[AMR][1000 genomes]
rs35057183	0.80[AMR][1000 genomes]
rs35124901	0.84[EUR][1000 genomes]
rs35255044	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35968359	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3748944	0.87[AMR][1000 genomes]
rs3828238	0.85[EUR][1000 genomes]
rs5012561	0.80[ASN][1000 genomes]
rs55923279	0.96[ASN][1000 genomes]
rs6753530	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6757006	0.80[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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv874160	chr2:55713102-55828974	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv521318	chr2:55716650-55736704	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv525434	chr2:55716650-55841640	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35189503	SMEK2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55718600-55726800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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