Variant report

Variant	rs3759890
Chromosome Location	chr15:45314594-45314595
allele	C/G
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	MAX	chr15:45314583-45316174	A549	lung:	n/a	chr15:45315775-45315784 chr15:45315773-45315786 chr15:45315775-45315785 chr15:45315774-45315785 chr15:45315766-45315782 chr15:45315776-45315783 chr15:45315774-45315785 chr15:45315764-45315773 chr15:45315775-45315784
2	POLR2A	chr15:45314499-45316225	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr15:45314566-45315040	K562	blood:	n/a	chr15:45314899-45314910
4	MAX	chr15:45314484-45316197	K562	blood:	n/a	chr15:45315775-45315784 chr15:45315773-45315786 chr15:45315775-45315785 chr15:45315774-45315785 chr15:45315766-45315782 chr15:45315776-45315783 chr15:45315774-45315785 chr15:45315764-45315773 chr15:45315775-45315784
5	E2F6	chr15:45314560-45316144	K562	blood:	n/a	chr15:45315640-45315650 chr15:45315634-45315644 chr15:45315262-45315271 chr15:45314899-45314910
6	E2F6	chr15:45314542-45316065	H1-hESC	embryonic stem cell:	n/a	chr15:45315640-45315650 chr15:45315634-45315644 chr15:45315262-45315271 chr15:45314899-45314910
7	ZNF143	chr15:45314591-45315654	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr15:45314551-45314970	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr15:45314533-45315002	H1-hESC	embryonic stem cell:	n/a	chr15:45314899-45314910
10	POLR2A	chr15:45314587-45315642	Raji	blood:	n/a	n/a
11	TEAD4	chr15:45314524-45315031	K562	blood:	n/a	n/a
12	HCFC1	chr15:45314502-45316447	Hela-S3	cervix:	n/a	n/a
13	CBX3	chr15:45314482-45315055	K562	blood:	n/a	n/a
14	CTCF	chr15:45314520-45314670	A549	lung:	n/a	n/a
15	MXI1	chr15:45314522-45316641	SK-N-SH	brain:	n/a	chr15:45314868-45314883
16	RAD21	chr15:45314577-45315006	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr15:45314560-45314710	HVMF	connective:	n/a	n/a

Variant related genes	Relation type
SORD	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11070436	1.00[CEU][hapmap]
rs11070439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11635836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636558	1.00[CEU][hapmap]
rs11637679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs12441189	1.00[CEU][hapmap]
rs12902552	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12902975	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs12903068	0.82[ASN][1000 genomes]
rs12913288	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[YRI][hapmap]
rs12916850	0.82[ASN][1000 genomes]
rs13380326	1.00[CEU][hapmap]
rs16976876	0.84[ASN][1000 genomes]
rs1704792	0.82[CEU][hapmap]
rs1720689	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs199334	0.90[EUR][1000 genomes]
rs2036831	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[YRI][hapmap]
rs2055858	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2217932	0.86[ASN][1000 genomes]
rs2470686	1.00[CEU][hapmap]
rs270822	0.83[EUR][1000 genomes]
rs34428536	0.94[ASN][1000 genomes]
rs35881035	0.95[ASN][1000 genomes]
rs3858900	0.95[ASN][1000 genomes]
rs452762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs58751943	0.82[ASN][1000 genomes]
rs6493131	1.00[CEU][hapmap]
rs67352586	0.84[ASN][1000 genomes]
rs71405285	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71478352	0.95[ASN][1000 genomes]
rs7169807	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72722052	0.94[ASN][1000 genomes]
rs8182070	0.84[ASN][1000 genomes]
rs925350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs963002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1048317	chr15:45152371-45326205	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv904184	chr15:45248787-45314764	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3759890	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3759890	SORD	cis	Skin Sun Exposed Lower leg	GTEx
rs3759890	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45312600-45314800	Enhancers	Stomach Mucosa	stomach
2	chr15:45313200-45314800	Enhancers	HepG2	liver
3	chr15:45313400-45314600	Weak transcription	Gastric	stomach
4	chr15:45313400-45314600	Weak transcription	Pancreas	Pancrea
5	chr15:45313600-45314600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:45313600-45314600	Enhancers	Duodenum Mucosa	Duodenum
7	chr15:45313800-45314600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr15:45313800-45314800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:45314000-45314600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:45314000-45314600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr15:45314200-45314600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr15:45314200-45314600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:45314400-45314600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr15:45314400-45314600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:45314400-45314600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:45314400-45314600	Enhancers	Primary B cells from cord blood	blood
17	chr15:45314400-45314600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:45314400-45314600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:45314400-45314600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr15:45314400-45314600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:45314400-45314600	Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr15:45314400-45314600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:45314400-45314600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:45314400-45314600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:45314400-45314600	Enhancers	Adipose Nuclei	Adipose
26	chr15:45314400-45314600	Enhancers	Liver	Liver
27	chr15:45314400-45314600	Enhancers	Brain Cingulate Gyrus	brain
28	chr15:45314400-45314600	Enhancers	Brain Substantia Nigra	brain
29	chr15:45314400-45314600	Enhancers	Right Ventricle	heart
30	chr15:45314400-45314600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:45314400-45314600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:45314400-45314600	Active TSS	Stomach Smooth Muscle	stomach
33	chr15:45314400-45314600	Enhancers	Dnd41	blood
34	chr15:45314400-45314600	Enhancers	HMEC	breast
35	chr15:45314400-45314600	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr15:45314400-45315000	Enhancers	Spleen	Spleen
37	chr15:45314400-45315000	Flanking Active TSS	Hela-S3	cervix
38	chr15:45314400-45316000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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