Variant report

Variant	rs2233375
Chromosome Location	chr2:233896498-233896499
allele	C/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	CTCF	chr2:233896380-233896530	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
NEU2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11681712	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11683026	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11692562	0.80[AMR][1000 genomes]
rs2233382	0.90[CEU][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2233394	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3935584	1.00[JPT][hapmap]
rs62191860	0.80[AMR][1000 genomes]
rs62193981	0.83[ASN][1000 genomes]
rs62193982	0.83[ASN][1000 genomes]
rs62193985	0.83[ASN][1000 genomes]
rs7558755	0.81[CEU][hapmap]
rs9653384	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv876009	chr2:233799400-233996429	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv876011	chr2:233809244-233912755	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Contrast sensitivity	24152035	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2233375	B3GNT7	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233864400-233902800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:233888400-233900200	Weak transcription	Esophagus	oesophagus
3	chr2:233891600-233898200	Weak transcription	NH-A	brain
4	chr2:233891600-233900200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:233891800-233896600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:233891800-233897000	Weak transcription	Osteobl	bone
7	chr2:233891800-233897200	Weak transcription	HMEC	breast
8	chr2:233892000-233898000	Weak transcription	NHEK	skin
9	chr2:233894200-233897400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:233894800-233898200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:233895200-233898000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:233895600-233897000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:233896200-233896600	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr2:233896200-233896800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr2:233896200-233897400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:233896200-233897600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:233896200-233897600	Enhancers	Fetal Muscle Leg	muscle
18	chr2:233896200-233897800	Enhancers	Fetal Muscle Trunk	muscle
19	chr2:233896400-233897000	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr2:233896400-233897200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr2:233896400-233897400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:233896400-233897400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:233896400-233898600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:233896400-233899000	Enhancers	HSMMtube	muscle

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