Variant report

Variant	rs577885555
Chromosome Location	chr4:20253064-20253065
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	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	KAP1	chr4:20251918-20253159	U2OS	brain:	n/a	n/a
4	MAX	chr4:20252951-20253935	H1-hESC	embryonic stem cell:	n/a	chr4:20253386-20253396
5	TBP	chr4:20252936-20254055	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr4:20253060-20253210	HPAF	blood vessel:	n/a	n/a
7	MAX	chr4:20252890-20253170	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr4:20252775-20254559	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
9	MAZ	chr4:20253041-20254964	IMR90	lung:	n/a	chr4:20253386-20253396
10	POLR2A	chr4:20253057-20255631	HEK293	kidney:	n/a	n/a
11	MAX	chr4:20252937-20253831	SK-N-SH	brain:	n/a	chr4:20253386-20253396
12	REST	chr4:20253052-20254957	H1-neurons	neurons:	n/a	chr4:20253730-20253748 chr4:20254048-20254061 chr4:20254554-20254574
13	NFIC	chr4:20252963-20253918	SK-N-SH	brain:	n/a	n/a
14	SIN3A	chr4:20252815-20254790	H1-hESC	embryonic stem cell:	n/a	chr4:20254076-20254085 chr4:20254559-20254573
15	MAX	chr4:20253060-20253887	SK-N-SH	brain:	n/a	chr4:20253386-20253396
16	PBX3	chr4:20253016-20254029	SK-N-SH	brain:	n/a	chr4:20253793-20253813
17	CTBP2	chr4:20252818-20254039	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr4:20253024-20254671	ECC-1	luminal epithelium:	n/a	chr4:20253386-20253396
19	POLR2A	chr4:20252952-20254235	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr4:20253048-20253700	H1-hESC	embryonic stem cell:	n/a	n/a
21	EGR1	chr4:20253063-20253846	ECC-1	luminal epithelium:	n/a	chr4:20253363-20253376 chr4:20253361-20253371 chr4:20253318-20253331
22	ZBTB7A	chr4:20252955-20253644	ECC-1	luminal epithelium:	n/a	chr4:20253322-20253331
23	EP300	chr4:20253050-20254288	SK-N-SH	brain:	n/a	chr4:20253508-20253517 chr4:20253068-20253082 chr4:20254057-20254066
24	POLR2A	chr4:20253044-20253991	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr4:20252992-20253985	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD2	chr4:20252935-20253747	Hela-S3	cervix:	n/a	n/a
27	TAF1	chr4:20253018-20253950	H1-hESC	embryonic stem cell:	n/a	n/a
28	TCF12	chr4:20253037-20254268	ECC-1	luminal epithelium:	n/a	chr4:20253418-20253425
29	EP300	chr4:20253021-20254374	ECC-1	luminal epithelium:	n/a	chr4:20253508-20253517 chr4:20253068-20253082 chr4:20254057-20254066
30	ZNF143	chr4:20253062-20253867	H1-hESC	embryonic stem cell:	n/a	chr4:20253507-20253517 chr4:20253706-20253724
31	POLR2A	chr4:20252924-20253831	PFSK-1	brain:	n/a	n/a

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

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

Extended variants
information (count: 3 )
Associated
traits (count: 0)

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:101 , 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	chr4:20252600-20253200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
7	chr4:20252600-20253200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:20252600-20253200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:20252600-20254200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:20252600-20254400	Active TSS	Right Atrium	heart
11	chr4:20252600-20255000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr4:20252600-20255000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:20252600-20255000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr4:20252600-20255600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:20252600-20257000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr4:20252600-20257200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr4:20252600-20257400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:20252600-20257800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:20252800-20253200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:20252800-20253200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:20252800-20253200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:20252800-20253200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:20252800-20253200	Flanking Active TSS	Liver	Liver
24	chr4:20252800-20253200	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr4:20252800-20253200	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr4:20252800-20253200	Flanking Active TSS	Fetal Brain Male	brain
27	chr4:20252800-20253200	Flanking Active TSS	Fetal Brain Female	brain
28	chr4:20252800-20253200	Flanking Active TSS	Fetal Heart	heart
29	chr4:20252800-20253200	Bivalent Enhancer	A549	lung
30	chr4:20252800-20253200	Flanking Active TSS	HUVEC	blood vessel
31	chr4:20252800-20253200	Flanking Active TSS	NH-A	brain
32	chr4:20252800-20253200	Flanking Active TSS	NHEK	skin
33	chr4:20252800-20253200	Flanking Active TSS	NHLF	lung
34	chr4:20252800-20253400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr4:20252800-20253600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:20252800-20253800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:20252800-20253800	Active TSS	Fetal Muscle Leg	muscle
38	chr4:20252800-20253800	Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr4:20252800-20253800	Active TSS	HMEC	breast
40	chr4:20252800-20254000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr4:20252800-20254000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:20252800-20254000	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr4:20252800-20254000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
44	chr4:20252800-20254000	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr4:20252800-20254000	Active TSS	Right Ventricle	heart
46	chr4:20252800-20254000	Active TSS	Stomach Smooth Muscle	stomach
47	chr4:20252800-20254200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr4:20252800-20254200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:20252800-20254200	Active TSS	Brain Substantia Nigra	brain
50	chr4:20252800-20254200	Bivalent/Poised TSS	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links