Variant report

Variant	rs938575
Chromosome Location	chr2:233768788-233768789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1083522	0.91[CEU][hapmap]
rs11535	0.88[CEU][hapmap]
rs13007579	0.83[ASN][1000 genomes]
rs2675954	0.91[CEU][hapmap]
rs2675955	0.85[EUR][1000 genomes]
rs2675968	0.87[CEU][hapmap]
rs4973569	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709937	0.87[CEU][hapmap]
rs748002	0.91[CEU][hapmap]
rs778341	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs778370	0.87[CEU][hapmap]
rs778371	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs938569	0.91[CEU][hapmap]

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	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
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3377192	chr2:233758324-233835472	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs938575	NGEF	cis	Esophagus Mucosa	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233757400-233776600	Weak transcription	Brain Angular Gyrus	brain
2	chr2:233758200-233768800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:233759200-233784400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:233764000-233768800	Weak transcription	Gastric	stomach
5	chr2:233764000-233783800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:233766600-233776400	Weak transcription	Liver	Liver
7	chr2:233767000-233772000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:233767000-233789000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:233767200-233771800	Weak transcription	HepG2	liver
10	chr2:233767200-233772000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:233767200-233776200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:233767200-233790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:233767400-233768800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:233767400-233769000	Enhancers	A549	lung
15	chr2:233767400-233771800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:233768600-233768800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:233768600-233769200	Strong transcription	Duodenum Mucosa	Duodenum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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