Variant report

Variant	rs352046
Chromosome Location	chr4:74864550-74864551
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	CTCF	chr4:74864480-74864630	HVMF	connective:	n/a	n/a
2	CTBP2	chr4:74863847-74864774	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr4:74863931-74864785	H1-hESC	embryonic stem cell:	n/a	chr4:74864560-74864574 chr4:74864725-74864737
4	CTCF	chr4:74864500-74864650	HUVEC	blood vessel:	n/a	n/a
5	JUND	chr4:74863967-74864749	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr4:74864540-74864690	HCFaa	heart:	n/a	n/a
7	RAD21	chr4:74864178-74864827	A549	lung:	n/a	chr4:74864560-74864574 chr4:74864725-74864737
8	RAD21	chr4:74864323-74864755	H1-hESC	embryonic stem cell:	n/a	chr4:74864560-74864574 chr4:74864725-74864737
9	ZNF143	chr4:74863893-74864803	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr4:74863986-74864725	A549	lung:	n/a	n/a
11	EP300	chr4:74864178-74864835	A549	lung:	n/a	n/a
12	CTCF	chr4:74864389-74864792	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr4:74864150-74864951	A549	lung:	n/a	n/a
14	CTCF	chr4:74864520-74864670	AG04450	lung:	n/a	n/a
15	ATF2	chr4:74863833-74864795	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr4:74864152-74864672	A549	lung:	n/a	n/a
17	BCL3	chr4:74864004-74864787	A549	lung:	n/a	chr4:74864475-74864484 chr4:74864621-74864629
18	POLR2A	chr4:74863792-74864744	H1-hESC	embryonic stem cell:	n/a	n/a
19	BCL3	chr4:74864089-74864845	A549	lung:	n/a	chr4:74864475-74864484 chr4:74864621-74864629
20	POLR2A	chr4:74863633-74864943	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr4:74863965-74864890	A549	lung:	n/a	chr4:74864175-74864184
22	TAF1	chr4:74863768-74864649	A549	lung:	n/a	n/a
23	CTCF	chr4:74864440-74864590	HRPEpiC	eye:	n/a	n/a
24	GTF2F1	chr4:74864046-74864796	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr4:74864322-74864884	A549	lung:	n/a	chr4:74864560-74864574 chr4:74864725-74864737
26	CTCF	chr4:74864540-74864690	HPF	lung:	n/a	n/a
27	GATA3	chr4:74863746-74864821	A549	lung:	n/a	n/a
28	CTCF	chr4:74864520-74864670	NHLF	lung:	n/a	n/a
29	CTCF	chr4:74864540-74864690	AoAF	blood vessel:	n/a	n/a
30	CTCF	chr4:74864540-74864690	HPAF	blood vessel:	n/a	n/a
31	SP1	chr4:74863929-74864762	A549	lung:	n/a	chr4:74864518-74864530 chr4:74864515-74864529 chr4:74864519-74864528
32	TAF1	chr4:74863773-74864780	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr4:74864540-74864690	HCPEpiC	choroid plexus:	n/a	n/a
34	CTCF	chr4:74864520-74864670	AG09319	gingival:	n/a	n/a
35	POLR2A	chr4:74863599-74864803	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr4:74864520-74864670	HA-sp	spinal cord:	n/a	n/a
37	CHD1	chr4:74863895-74864748	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr4:74864490-74864726	Fibrobl	skin:	n/a	n/a
39	HDAC2	chr4:74864301-74864784	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr4:74864500-74864650	HFF	foreskin:	n/a	n/a
41	SIN3A	chr4:74863843-74864760	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:74863836-74864762	A549	lung:	n/a	n/a
43	MAX	chr4:74863988-74864822	H1-hESC	embryonic stem cell:	n/a	chr4:74864175-74864184
44	CTCF	chr4:74864520-74864670	HAc	cerebellar:	n/a	n/a
45	MAX	chr4:74863686-74864994	A549	lung:	n/a	chr4:74864175-74864184
46	MYC	chr4:74863508-74865118	A549	lung:	n/a	chr4:74864175-74864184
47	RAD21	chr4:74864300-74864873	A549	lung:	n/a	chr4:74864560-74864574 chr4:74864725-74864737
48	USF2	chr4:74863891-74864769	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr4:74864520-74864670	HRPEpiC	eye:	n/a	n/a
50	MAX	chr4:74863820-74864925	H1-hESC	embryonic stem cell:	n/a	chr4:74864175-74864184

Variant related genes	Relation type
CXCL5	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs168449	0.86[EUR][1000 genomes]
rs183028	0.86[EUR][1000 genomes]
rs187080	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs187082	0.93[EUR][1000 genomes]
rs191601	0.86[EUR][1000 genomes]
rs193263	0.86[EUR][1000 genomes]
rs2437285	0.91[EUR][1000 genomes]
rs2457996	0.86[EUR][1000 genomes]
rs2564594	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs352007	0.86[EUR][1000 genomes]
rs352009	0.86[EUR][1000 genomes]
rs352010	0.81[EUR][1000 genomes]
rs352045	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352047	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs377579	0.86[EUR][1000 genomes]
rs394408	0.86[EUR][1000 genomes]
rs409336	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs420389	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs425535	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426901	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs440676	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs442155	0.82[EUR][1000 genomes]
rs447206	0.84[EUR][1000 genomes]
rs450373	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs552582	0.84[EUR][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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74861600-74864800	Active TSS	A549	lung
2	chr4:74861800-74865000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr4:74862800-74865000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr4:74863000-74864800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr4:74863400-74864600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:74863600-74864800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:74863800-74864600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr4:74863800-74864600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr4:74863800-74864600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:74863800-74864600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:74863800-74864600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:74863800-74864600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
13	chr4:74863800-74864600	Bivalent Enhancer	Fetal Lung	lung
14	chr4:74863800-74864600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
15	chr4:74863800-74864600	Flanking Active TSS	HUVEC	blood vessel
16	chr4:74863800-74864600	Active TSS	NHLF	lung
17	chr4:74863800-74864800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:74863800-74864800	Enhancers	Liver	Liver
19	chr4:74863800-74864800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:74863800-74864800	Bivalent/Poised TSS	Fetal Brain Female	brain
21	chr4:74864000-74864600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:74864000-74864600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:74864000-74864600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:74864000-74864600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:74864000-74864600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:74864000-74864600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:74864000-74864600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:74864000-74864600	Active TSS	Brain Angular Gyrus	brain
29	chr4:74864000-74864600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:74864000-74864600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr4:74864000-74864600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr4:74864000-74864600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
33	chr4:74864000-74864600	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr4:74864000-74864600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
35	chr4:74864000-74864600	Bivalent/Poised TSS	Left Ventricle	heart
36	chr4:74864000-74864600	Active TSS	Rectal Smooth Muscle	rectum
37	chr4:74864000-74864600	Active TSS	Right Atrium	heart
38	chr4:74864000-74864600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
39	chr4:74864000-74864600	Enhancers	HMEC	breast
40	chr4:74864000-74864600	Active TSS	HSMM	muscle
41	chr4:74864000-74864600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr4:74864000-74864600	Active TSS	NH-A	brain
43	chr4:74864000-74864800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:74864000-74864800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:74864000-74864800	Active TSS	Brain Anterior Caudate	brain
46	chr4:74864000-74870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:74864200-74864600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr4:74864200-74864600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:74864200-74864600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr4:74864200-74864600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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