Variant report

Variant	rs2279737
Chromosome Location	chr5:58334645-58334646
allele	A/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	MYC	chr5:58333738-58337715	A549	lung:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337561-58337571 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
2	CTCF	chr5:58334500-58334650	HRPEpiC	eye:	n/a	n/a
3	POLR2A	chr5:58334257-58336743	PFSK-1	brain:	n/a	n/a
4	CTBP2	chr5:58334577-58336052	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr5:58334554-58335885	H1-neurons	neurons:	n/a	n/a
6	CTCF	chr5:58334640-58334790	Caco-2	colon:	n/a	n/a
7	CTCF	chr5:58334482-58334808	GM12878	blood:	n/a	n/a
8	ATF3	chr5:58333802-58335020	A549	lung:	n/a	n/a
9	ZNF143	chr5:58334485-58334790	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr5:58334405-58337505	NB4	blood:	n/a	chr5:58336788-58336797 chr5:58336783-58336802 chr5:58336206-58336221 chr5:58336787-58336798 chr5:58337236-58337245 chr5:58336786-58336799 chr5:58336788-58336798 chr5:58336788-58336798 chr5:58336791-58336799 chr5:58336206-58336216 chr5:58336787-58336798
11	SP4	chr5:58334503-58334749	H1-hESC	embryonic stem cell:	n/a	n/a
12	RAD21	chr5:58334474-58334938	H1-hESC	embryonic stem cell:	n/a	chr5:58334650-58334660
13	CTCF	chr5:58334500-58334650	AG09319	gingival:	n/a	n/a
14	MYC	chr5:58333863-58336853	NB4	blood:	n/a	chr5:58336786-58336799 chr5:58336783-58336802 chr5:58336788-58336798 chr5:58336206-58336221 chr5:58336788-58336797 chr5:58336206-58336216 chr5:58336787-58336798 chr5:58336788-58336798 chr5:58336787-58336798 chr5:58336791-58336799
15	CTCF	chr5:58334560-58334710	AG09319	gingival:	n/a	n/a
16	GATA3	chr5:58334373-58336526	A549	lung:	n/a	n/a
17	POLR2A	chr5:58334348-58335954	A549	lung:	n/a	n/a
18	CTCF	chr5:58334500-58334650	AG04449	skin:	n/a	n/a
19	CTCF	chr5:58334580-58334730	HBMEC	blood vessel:	n/a	n/a
20	ELF1	chr5:58334020-58335031	A549	lung:	n/a	n/a
21	SIN3AK20	chr5:58333591-58334792	A549	lung:	n/a	n/a
22	RAD21	chr5:58334394-58334915	H1-hESC	embryonic stem cell:	n/a	chr5:58334650-58334660
23	YY1	chr5:58334381-58334983	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr5:58334602-58334708	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF263	chr5:58334295-58335857	HEK293-T-REx	kidney:	n/a	n/a
26	FOSL2	chr5:58333394-58334913	A549	lung:	n/a	n/a
27	POLR2A	chr5:58333046-58336833	A549	lung:	n/a	n/a
28	SIX5	chr5:58330273-58336780	A549	lung:	n/a	chr5:58334021-58334030
29	MXI1	chr5:58334320-58335914	IMR90	lung:	n/a	n/a
30	CTCF	chr5:58334540-58334690	NB4	blood:	n/a	n/a
31	REST	chr5:58331372-58337614	A549	lung:	n/a	chr5:58334044-58334052 chr5:58335557-58335570
32	RAD21	chr5:58334540-58334767	SK-N-SH_RA	brain:	n/a	chr5:58334650-58334660
33	MXI1	chr5:58334271-58336440	SK-N-SH	brain:	n/a	n/a
34	CTCF	chr5:58334590-58334697	GM10248	blood:	n/a	n/a
35	REST	chr5:58334254-58336042	H1-neurons	neurons:	n/a	chr5:58335557-58335570
36	SP1	chr5:58331577-58338881	A549	lung:	n/a	chr5:58333512-58333519 chr5:58335988-58335997
37	RAD21	chr5:58334498-58334713	SK-N-SH_RA	brain:	n/a	chr5:58334650-58334660
38	POLR2A	chr5:58331579-58336345	IMR90	lung:	n/a	n/a
39	FOXP2	chr5:58334594-58335902	PFSK-1	brain:	n/a	n/a
40	SIN3A	chr5:58334564-58335889	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr5:58334182-58336389	A549	lung:	n/a	n/a
42	CTCF	chr5:58334580-58334730	HCPEpiC	choroid plexus:	n/a	n/a
43	TAF1	chr5:58332948-58336675	A549	lung:	n/a	n/a
44	CTCF	chr5:58334623-58334691	Lung_OC	lung:	n/a	n/a
45	POLR2A	chr5:58334487-58336050	A549	lung:	n/a	n/a
46	CTCF	chr5:58334580-58334730	BE2_C	brain:	n/a	n/a
47	POLR2A	chr5:58333901-58336586	NB4	blood:	n/a	n/a
48	POLR2A	chr5:58332062-58336640	MCF10A-Er-Src	breast:	n/a	n/a
49	BCL3	chr5:58333566-58336736	A549	lung:	n/a	chr5:58335393-58335406 chr5:58336423-58336432 chr5:58335440-58335453
50	RAD21	chr5:58334557-58335856	IMR90	lung:	n/a	chr5:58334650-58334660

Variant related genes	Relation type
ENSG00000247345	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10514871	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1498602	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1498607	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1498609	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17719378	0.81[TSI][hapmap]
rs17720311	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17776777	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17776825	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17777617	0.81[GIH][hapmap]
rs55946132	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55970459	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56057207	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62358506	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72770683	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279737	C5orf35	cis	cerebellum	SCAN
rs2279737	GRID2	trans	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58330400-58336400	Active TSS	Right Ventricle	heart
2	chr5:58330400-58336600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:58330600-58335000	Transcr. at gene 5' and 3'	A549	lung
4	chr5:58330600-58336200	Active TSS	Right Atrium	heart
5	chr5:58330800-58335800	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr5:58331000-58336200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:58331000-58336400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:58331000-58336600	Active TSS	Psoas Muscle	Psoas
9	chr5:58332000-58334800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr5:58332000-58335200	Active TSS	Placenta Amnion	Placenta Amnion
11	chr5:58332000-58335800	Active TSS	HSMM	muscle
12	chr5:58332400-58335000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:58332800-58334800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:58333000-58334800	Flanking Active TSS	NHEK	skin
15	chr5:58333000-58335000	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr5:58333000-58335800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:58333000-58336200	Active TSS	Left Ventricle	heart
18	chr5:58333200-58336000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr5:58333400-58334800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:58333400-58334800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr5:58333400-58334800	Flanking Active TSS	Hela-S3	cervix
22	chr5:58333400-58336000	Active TSS	Lung	lung
23	chr5:58333400-58336200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:58333600-58334800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:58333600-58335000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr5:58333600-58335800	Active TSS	Primary T cells from cord blood	blood
27	chr5:58333600-58335800	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr5:58333600-58336000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr5:58333600-58336000	Active TSS	Small Intestine	intestine
30	chr5:58333600-58336400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr5:58333800-58334800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:58333800-58334800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
33	chr5:58333800-58334800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr5:58333800-58334800	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr5:58333800-58334800	Flanking Active TSS	Fetal Lung	lung
36	chr5:58333800-58334800	Flanking Active TSS	Fetal Thymus	thymus
37	chr5:58333800-58334800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr5:58333800-58335000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:58333800-58335000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr5:58333800-58335000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:58333800-58335000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr5:58333800-58335600	Active TSS	Muscle Satellite Cultured Cells	--
43	chr5:58333800-58335800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr5:58333800-58336000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr5:58334000-58335000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:58334000-58335400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:58334000-58335600	Bivalent/Poised TSS	HepG2	liver
48	chr5:58334000-58335800	Active TSS	NHLF	lung
49	chr5:58334000-58336000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:58334000-58336000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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