Variant report

Variant	rs1323065
Chromosome Location	chr4:20253977-20253978
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	ZBTB7A	chr4:20253025-20254617	ECC-1	luminal epithelium:	n/a	chr4:20253322-20253331 chr4:20253750-20253758
2	TAF1	chr4:20253060-20254152	ECC-1	luminal epithelium:	n/a	n/a
3	JUND	chr4:20253134-20254055	H1-hESC	embryonic stem cell:	n/a	chr4:20253775-20253789
4	ZNF263	chr4:20253709-20255153	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr4:20253209-20254030	HUVEC	blood vessel:	n/a	n/a
6	TBP	chr4:20252936-20254055	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAX	chr4:20252775-20254559	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
8	MAZ	chr4:20253041-20254964	IMR90	lung:	n/a	chr4:20253386-20253396
9	POLR2A	chr4:20253057-20255631	HEK293	kidney:	n/a	n/a
10	E2F6	chr4:20253404-20254076	H1-hESC	embryonic stem cell:	n/a	chr4:20253770-20253779 chr4:20253508-20253517 chr4:20253444-20253453
11	POLR2A	chr4:20253330-20255237	H1-neurons	neurons:	n/a	n/a
12	POLR2A	chr4:20253112-20254794	ECC-1	luminal epithelium:	n/a	n/a
13	REST	chr4:20253052-20254957	H1-neurons	neurons:	n/a	chr4:20253730-20253748 chr4:20254048-20254061 chr4:20254554-20254574
14	SMC3	chr4:20253245-20254155	Hela-S3	cervix:	n/a	chr4:20253441-20253451 chr4:20254081-20254091
15	TCF12	chr4:20253255-20254174	ECC-1	luminal epithelium:	n/a	chr4:20253418-20253425
16	HA-E2F1	chr4:20253163-20254221	Hela-S3	cervix:	n/a	chr4:20253349-20253358 chr4:20253770-20253779 chr4:20253508-20253517 chr4:20253357-20253367 chr4:20253444-20253453
17	E2F6	chr4:20253194-20254243	H1-hESC	embryonic stem cell:	n/a	chr4:20253349-20253358 chr4:20253770-20253779 chr4:20253508-20253517 chr4:20253357-20253367 chr4:20253444-20253453
18	SIN3A	chr4:20252815-20254790	H1-hESC	embryonic stem cell:	n/a	chr4:20254076-20254085 chr4:20254559-20254573
19	POLR2A	chr4:20253214-20254016	MCF-7	breast:	n/a	n/a
20	PBX3	chr4:20253016-20254029	SK-N-SH	brain:	n/a	chr4:20253793-20253813
21	CTBP2	chr4:20252818-20254039	H1-hESC	embryonic stem cell:	n/a	n/a
22	SUZ12	chr4:20253936-20257122	NT2-D1	testis:	n/a	n/a
23	MAX	chr4:20253024-20254671	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
24	POLR2A	chr4:20252952-20254235	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr4:20253916-20255139	H1-neurons	neurons:	n/a	n/a
26	ZBTB7A	chr4:20253893-20254666	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr4:20253277-20254062	IMR90	lung:	n/a	n/a
28	EP300	chr4:20253050-20254288	SK-N-SH	brain:	n/a	chr4:20253508-20253517 chr4:20253068-20253082 chr4:20254057-20254066
29	POLR2A	chr4:20253044-20253991	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr4:20252992-20253985	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr4:20253180-20254618	Hela-S3	cervix:	n/a	n/a
32	MAX	chr4:20253218-20254266	Hela-S3	cervix:	n/a	chr4:20253386-20253396
33	TCF12	chr4:20253037-20254268	ECC-1	luminal epithelium:	n/a	chr4:20253418-20253425
34	EP300	chr4:20253021-20254374	ECC-1	luminal epithelium:	n/a	chr4:20253508-20253517 chr4:20253068-20253082 chr4:20254057-20254066

No.	Distal block	Cell Line	Cell type
1	chr4:20252458..20255013-chr4:20255238..20258452,3	MCF-7	breast:
2	chr4:20252097..20254985-chr4:20256141..20260392,5	MCF-7	breast:
3	chr4:20025908..20028659-chr4:20253195..20254796,2	MCF-7	breast:

Variant related genes	Relation type
SLIT2	TF binding region
ENSG00000145147	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2575077	1.00[ASN][1000 genomes]
rs2760134	1.00[ASN][1000 genomes]
rs4552453	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508726	1.00[ASN][1000 genomes]
rs527371	1.00[ASN][1000 genomes]
rs529193	1.00[ASN][1000 genomes]
rs593943	1.00[ASN][1000 genomes]
rs611907	1.00[ASN][1000 genomes]
rs615576	1.00[ASN][1000 genomes]
rs624354	1.00[ASN][1000 genomes]
rs625909	1.00[ASN][1000 genomes]
rs643189	1.00[ASN][1000 genomes]
rs643562	1.00[ASN][1000 genomes]
rs7655084	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7685284	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793380	1.00[ASN][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	nsv878736	chr4:20233035-20279858	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv878737	chr4:20233035-20282334	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3373550	chr4:20252479-20255027	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20252200-20258200	Active TSS	NHDF-Ad	bronchial
2	chr4:20252400-20255200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:20252400-20256400	Active TSS	Brain Anterior Caudate	brain
4	chr4:20252400-20257000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr4:20252400-20257400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:20252600-20254200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:20252600-20254400	Active TSS	Right Atrium	heart
8	chr4:20252600-20255000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr4:20252600-20255000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr4:20252600-20255000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:20252600-20255600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:20252600-20257000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr4:20252600-20257200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:20252600-20257400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:20252600-20257800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:20252800-20254000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:20252800-20254000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:20252800-20254000	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr4:20252800-20254000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
20	chr4:20252800-20254000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr4:20252800-20254000	Active TSS	Right Ventricle	heart
22	chr4:20252800-20254000	Active TSS	Stomach Smooth Muscle	stomach
23	chr4:20252800-20254200	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr4:20252800-20254200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:20252800-20254200	Active TSS	Brain Substantia Nigra	brain
26	chr4:20252800-20254200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
27	chr4:20252800-20254200	Active TSS	Ovary	ovary
28	chr4:20252800-20254400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
29	chr4:20252800-20254400	Active TSS	Fetal Kidney	kidney
30	chr4:20252800-20254400	Active TSS	Rectal Smooth Muscle	rectum
31	chr4:20252800-20254800	Active TSS	Left Ventricle	heart
32	chr4:20252800-20257000	Active TSS	Osteobl	bone
33	chr4:20252800-20258600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:20253000-20254000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:20253000-20254000	Bivalent/Poised TSS	Esophagus	oesophagus
36	chr4:20253000-20254000	Active TSS	Pancreas	Pancrea
37	chr4:20253000-20254000	Active TSS	Psoas Muscle	Psoas
38	chr4:20253000-20254000	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr4:20253000-20254000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:20253000-20254000	Bivalent/Poised TSS	Spleen	Spleen
41	chr4:20253000-20254000	Active TSS	HSMM	muscle
42	chr4:20253000-20254200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:20253000-20254200	Active TSS	Fetal Lung	lung
44	chr4:20253000-20254200	Active TSS	HSMMtube	muscle
45	chr4:20253000-20254400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr4:20253000-20254400	Active TSS	Brain Hippocampus Middle	brain
47	chr4:20253000-20254600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:20253000-20254600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
49	chr4:20253000-20255200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr4:20253000-20256600	Bivalent/Poised TSS	Thymus	Thymus

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