Variant report

Variant	rs4319975
Chromosome Location	chr2:48959603-48959604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12998409	1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4074647	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4074648	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4596023	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4953625	1.00[MEX][hapmap]
rs7563144	1.00[MEX][hapmap]
rs9798043	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv817851	chr2:48941428-48973127	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3411434	chr2:48959544-48959703	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4319975	BEX1	trans	parietal	SCAN
rs4319975	LHCGR	cis	Esophagus Muscularis	GTEx
rs4319975	LHCGR	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48950600-48960400	Weak transcription	Ovary	ovary
2	chr2:48955600-48960400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:48956000-48959800	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:48956400-48960000	Weak transcription	Fetal Stomach	stomach
5	chr2:48956800-48960200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:48957000-48959800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:48957000-48960000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:48957000-48960200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:48957800-48960400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:48957800-48960400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:48957800-48960400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:48957800-48960400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:48958000-48960000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:48958000-48960200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:48959200-48959800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:48959400-48959800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:48959600-48959800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr2:48959600-48961800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:48959600-48963200	Enhancers	Adipose Nuclei	Adipose

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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