Variant report

Variant	rs2593079
Chromosome Location	chr4:56776848-56776849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10007247	0.85[ASN][1000 genomes]
rs1838928	0.91[JPT][hapmap];0.82[MEX][hapmap]
rs2593068	0.86[CHD][hapmap]
rs2593082	0.86[CHD][hapmap]
rs2593085	0.86[CHD][hapmap]
rs2702327	0.86[CHD][hapmap]
rs4128946	0.83[CHD][hapmap]
rs4479769	0.86[CHD][hapmap]
rs4526032	0.86[CHD][hapmap]
rs6857163	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv3406311	chr4:56580578-56840877	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv427681	chr4:56651921-56908209	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv879024	chr4:56742205-56786589	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv879025	chr4:56742205-56808607	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2593079	TXNDC9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56766800-56786800	Weak transcription	Ovary	ovary
2	chr4:56770800-56777800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr4:56771000-56779800	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:56772000-56786600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:56772600-56784800	Weak transcription	Primary T cells from cord blood	blood
6	chr4:56772800-56793200	Weak transcription	Left Ventricle	heart
7	chr4:56773600-56788200	Weak transcription	Right Atrium	heart
8	chr4:56773800-56778000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:56774000-56778200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:56774000-56803200	Weak transcription	HUVEC	blood vessel
11	chr4:56774200-56786400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:56774400-56778200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:56776200-56777000	Enhancers	NHDF-Ad	bronchial
14	chr4:56776400-56777200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:56776600-56777000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:56776600-56777000	Enhancers	Osteobl	bone
17	chr4:56776800-56777000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:56776800-56778000	Weak transcription	NHEK	skin
19	chr4:56776800-56778200	Weak transcription	HMEC	breast

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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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