Variant report

Variant	rs58537556
Chromosome Location	chr4:16510866-16510867
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	CTCF	chr4:16510780-16510930	HEK293	kidney:	n/a	chr4:16510780-16510801
2	CTCF	chr4:16510760-16510910	SAEC	small airway:	n/a	chr4:16510780-16510801
3	CBX3	chr4:16510661-16511029	HCT-116	colon:	n/a	n/a
4	CTCF	chr4:16510720-16510870	GM12864	blood:	n/a	chr4:16510780-16510801
5	CTCF	chr4:16510800-16510950	K562	blood:	n/a	n/a
6	CTCF	chr4:16510760-16510910	GM12868	blood:	n/a	chr4:16510780-16510801
7	CTCF	chr4:16510740-16510890	GM12866	blood:	n/a	chr4:16510780-16510801
8	CTCF	chr4:16510720-16510870	HEEpiC	esophagus:	n/a	chr4:16510780-16510801
9	CTCF	chr4:16510740-16510890	AG04450	lung:	n/a	chr4:16510780-16510801
10	CTCF	chr4:16510720-16510870	HMEC	breast:	n/a	chr4:16510780-16510801
11	ZNF143	chr4:16510627-16510967	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr4:16510740-16510890	GM12869	blood:	n/a	chr4:16510780-16510801
13	CTCF	chr4:16510740-16510890	BJ	skin:	n/a	chr4:16510780-16510801
14	CTCF	chr4:16510760-16510910	HL-60	blood:	n/a	chr4:16510780-16510801
15	CTCF	chr4:16510720-16510870	HRPEpiC	eye:	n/a	chr4:16510780-16510801
16	CTCF	chr4:16510628-16510922	K562	blood:	n/a	chr4:16510780-16510801
17	CTCF	chr4:16510720-16510870	HEK293	kidney:	n/a	chr4:16510780-16510801
18	CBX3	chr4:16510655-16510932	K562	blood:	n/a	n/a
19	CTCF	chr4:16510720-16510870	AG09309	skin:	n/a	chr4:16510780-16510801
20	CTCF	chr4:16510760-16510910	HRE	kidney:	n/a	chr4:16510780-16510801
21	RAD21	chr4:16510675-16510934	H1-hESC	embryonic stem cell:	n/a	chr4:16510783-16510802
22	RAD21	chr4:16510546-16510986	HCT-116	colon:	n/a	chr4:16510783-16510802
23	CTCF	chr4:16510720-16510870	AG04450	lung:	n/a	chr4:16510780-16510801
24	CBX3	chr4:16510599-16510898	K562	blood:	n/a	n/a
25	CTCF	chr4:16510720-16510870	HPAF	blood vessel:	n/a	chr4:16510780-16510801
26	CTCF	chr4:16510720-16510870	WERI-Rb-1	eye:	n/a	chr4:16510780-16510801
27	CTCF	chr4:16510740-16510890	HFF	foreskin:	n/a	chr4:16510780-16510801
28	CTCF	chr4:16510760-16510910	GM12873	blood:	n/a	chr4:16510780-16510801
29	CTCF	chr4:16510720-16510870	RPTEC	kidney:	n/a	chr4:16510780-16510801
30	CTCF	chr4:16510760-16510910	HEEpiC	esophagus:	n/a	chr4:16510780-16510801
31	CTCF	chr4:16510720-16510870	HBMEC	blood vessel:	n/a	chr4:16510780-16510801
32	CTCF	chr4:16510730-16510886	GM13977	blood:	n/a	chr4:16510780-16510801
33	KAP1	chr4:16510636-16511014	K562	blood:	n/a	n/a
34	CTCF	chr4:16510720-16510870	A549	lung:	n/a	chr4:16510780-16510801
35	CTCF	chr4:16510740-16510890	HMF	breast:	n/a	chr4:16510780-16510801
36	CTCF	chr4:16510740-16510890	BE2_C	brain:	n/a	chr4:16510780-16510801
37	CTCF	chr4:16510714-16510890	Hela-S3	cervix:	n/a	chr4:16510780-16510801
38	CTCF	chr4:16510720-16510870	AG09319	gingival:	n/a	chr4:16510780-16510801
39	CTCF	chr4:16510720-16510870	GM12867	blood:	n/a	chr4:16510780-16510801
40	CTCF	chr4:16510720-16510870	NB4	blood:	n/a	chr4:16510780-16510801
41	CTCF	chr4:16510820-16510970	WI-38	lung:	n/a	n/a
42	CTCF	chr4:16510720-16510870	GM12869	blood:	n/a	chr4:16510780-16510801
43	CTCF	chr4:16510740-16510890	HCT-116	colon:	n/a	chr4:16510780-16510801
44	CTCF	chr4:16510673-16510921	HUVEC	blood vessel:	n/a	chr4:16510780-16510801
45	CTCF	chr4:16510740-16510890	AG09319	gingival:	n/a	chr4:16510780-16510801
46	CTCF	chr4:16510740-16510890	GM12865	blood:	n/a	chr4:16510780-16510801
47	CTCF	chr4:16510677-16510916	H1-hESC	embryonic stem cell:	n/a	chr4:16510780-16510801
48	ZNF143	chr4:16510653-16510948	K562	blood:	n/a	n/a
49	SETDB1	chr4:16510627-16510988	U2OS	brain:	n/a	n/a
50	CTCF	chr4:16510708-16510879	MCF-7	breast:	n/a	chr4:16510780-16510801

Variant related genes	Relation type
LDB2	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3805319	0.81[AFR][1000 genomes]
rs73115968	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73115969	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73798737	1.00[EUR][1000 genomes]
rs7666923	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv428755	chr4:16366311-16528135	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16498400-16513200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:16498400-16518200	Weak transcription	Brain Angular Gyrus	brain
3	chr4:16501400-16511400	Weak transcription	Gastric	stomach
4	chr4:16502200-16512200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:16502800-16511400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:16502800-16512200	Weak transcription	Pancreas	Pancrea
7	chr4:16503000-16511200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:16503000-16511400	Weak transcription	Right Ventricle	heart
9	chr4:16503000-16513000	Weak transcription	Primary T cells from cord blood	blood
10	chr4:16503200-16518400	Weak transcription	Brain Substantia Nigra	brain
11	chr4:16504600-16511400	Weak transcription	Esophagus	oesophagus
12	chr4:16504600-16511600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:16505400-16513400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:16505400-16522200	Weak transcription	Lung	lung
15	chr4:16505800-16512000	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:16506400-16514600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:16507400-16511400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:16508200-16511400	Strong transcription	Ovary	ovary
19	chr4:16509000-16512200	Strong transcription	Osteobl	bone
20	chr4:16509200-16511600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:16509200-16514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:16509600-16511600	ZNF genes & repeats	Fetal Muscle Leg	muscle
23	chr4:16510000-16515800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:16510200-16511400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:16510200-16512000	Strong transcription	Fetal Kidney	kidney
26	chr4:16510200-16518200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr4:16510400-16511400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:16510400-16511400	Weak transcription	Left Ventricle	heart
29	chr4:16510400-16511400	Weak transcription	Spleen	Spleen
30	chr4:16510400-16511800	Weak transcription	Adipose Nuclei	Adipose
31	chr4:16510400-16518200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:16510600-16511200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:16510600-16511400	Weak transcription	Fetal Stomach	stomach
34	chr4:16510600-16511800	ZNF genes & repeats	HUVEC	blood vessel
35	chr4:16510600-16512400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
36	chr4:16510600-16512400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr4:16510800-16511000	ZNF genes & repeats	ES-WA7 Cell Line	embryonic stem cell
38	chr4:16510800-16511000	ZNF genes & repeats	Liver	Liver
39	chr4:16510800-16511200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:16510800-16511600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:16510800-16511600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
42	chr4:16510800-16512200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
43	chr4:16510800-16512200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:16510800-16512200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr4:16510800-16512200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
46	chr4:16510800-16512400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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