Variant report

Variant	rs10020333
Chromosome Location	chr4:106817221-106817222
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	EGR1	chr4:106817071-106817331	GM12878	blood:	n/a	chr4:106817193-106817207 chr4:106817098-106817108
2	RAD21	chr4:106816796-106817857	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:106817047-106817939	H1-neurons	neurons:	n/a	n/a
4	ZBTB7A	chr4:106815992-106817345	ECC-1	luminal epithelium:	n/a	chr4:106816744-106816755
5	CTBP2	chr4:106815602-106817837	H1-hESC	embryonic stem cell:	n/a	n/a
6	PML	chr4:106815939-106818208	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:106816111-106817950	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:106816132-106817974	GM18526	blood:	n/a	n/a
9	CREB1	chr4:106816933-106817854	GM12878	blood:	n/a	n/a
10	RUNX3	chr4:106815766-106818157	GM12878	blood:	n/a	n/a
11	ZNF263	chr4:106815627-106817896	HEK293-T-REx	kidney:	n/a	chr4:106816907-106816916
12	PAX5	chr4:106816876-106817334	GM12892	blood:	n/a	n/a
13	HA-E2F1	chr4:106815880-106818135	MCF-7	breast:	n/a	chr4:106816088-106816095 chr4:106816519-106816528 chr4:106817591-106817603 chr4:106817064-106817078 chr4:106817215-106817223 chr4:106816543-106816553 chr4:106817216-106817223 chr4:106816088-106816095 chr4:106817216-106817223 chr4:106816088-106816095 chr4:106817216-106817223 chr4:106817215-106817224 chr4:106816908-106816923 chr4:106817215-106817223 chr4:106817067-106817081
14	FOXM1	chr4:106816935-106817582	GM12878	blood:	n/a	n/a
15	BCLAF1	chr4:106817065-106817847	GM12878	blood:	n/a	chr4:106817236-106817245
16	ZNF143	chr4:106816635-106817577	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:106816113-106817811	GM12878	blood:	n/a	n/a
18	CTCF	chr4:106817140-106817290	SAEC	small airway:	n/a	n/a
19	GATA3	chr4:106816618-106818819	MCF-7	breast:	n/a	chr4:106818035-106818047 chr4:106818036-106818045 chr4:106818038-106818045 chr4:106818036-106818046
20	NFIC	chr4:106816445-106817721	GM12878	blood:	n/a	n/a
21	PML	chr4:106817177-106817331	GM12878	blood:	n/a	n/a
22	POLR2A	chr4:106816140-106817693	GM18505	blood:	n/a	n/a
23	POLR2A	chr4:106816078-106818016	GM19099	blood:	n/a	n/a
24	ZBTB7A	chr4:106816017-106817323	ECC-1	luminal epithelium:	n/a	chr4:106816744-106816755
25	FOXM1	chr4:106816988-106817496	GM12878	blood:	n/a	n/a
26	HDAC2	chr4:106816033-106817309	MCF-7	breast:	n/a	n/a
27	E2F6	chr4:106815969-106817807	H1-hESC	embryonic stem cell:	n/a	chr4:106816088-106816095 chr4:106816519-106816528 chr4:106817591-106817603 chr4:106817064-106817078 chr4:106817215-106817223 chr4:106816543-106816553 chr4:106817216-106817223 chr4:106816088-106816095 chr4:106817216-106817223 chr4:106816088-106816095 chr4:106817216-106817223 chr4:106817215-106817224 chr4:106816908-106816923 chr4:106817215-106817223 chr4:106817067-106817081
28	MTA3	chr4:106817118-106818043	GM12878	blood:	n/a	n/a
29	ELF1	chr4:106816067-106817888	GM12878	blood:	n/a	chr4:106817301-106817313 chr4:106816206-106816218 chr4:106816617-106816629
30	RUNX3	chr4:106816720-106817732	GM12878	blood:	n/a	n/a
31	SIN3A	chr4:106817217-106817934	H1-hESC	embryonic stem cell:	n/a	n/a
32	MTA3	chr4:106815901-106818134	GM12878	blood:	n/a	n/a
33	BCL3	chr4:106817113-106817684	GM12878	blood:	n/a	chr4:106817236-106817245
34	STAT5A	chr4:106816543-106817843	GM12878	blood:	n/a	n/a
35	SUZ12	chr4:106816071-106817788	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr4:106816107-106817844	MCF-7	breast:	n/a	n/a
37	E2F6	chr4:106816557-106817375	H1-hESC	embryonic stem cell:	n/a	chr4:106817064-106817078 chr4:106817215-106817223 chr4:106817216-106817223 chr4:106817216-106817223 chr4:106817216-106817223 chr4:106817215-106817224 chr4:106816908-106816923 chr4:106817215-106817223 chr4:106817067-106817081
38	POLR2A	chr4:106816128-106817776	GM12878	blood:	n/a	n/a
39	POLR2A	chr4:106816074-106817749	GM12892	blood:	n/a	n/a
40	SIN3AK20	chr4:106815818-106818678	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106393662..106395828-chr4:106816451..106818779,3	MCF-7	breast:
2	chr4:106628392..106631014-chr4:106816298..106818181,3	MCF-7	breast:

Variant related genes	Relation type
NPNT	TF binding region
INTS12	TF binding region
ENSG00000138785	Chromatin interaction
ENSG00000138777	Chromatin interaction
ENSG00000138780	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs2553440	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106815400-106818200	Active TSS	Duodenum Mucosa	Duodenum
2	chr4:106815600-106817400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr4:106815600-106818000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:106815800-106817400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:106815800-106817600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:106815800-106817600	Active TSS	Fetal Kidney	kidney
7	chr4:106815800-106817800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr4:106815800-106817800	Active TSS	Pancreas	Pancrea
9	chr4:106815800-106818000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr4:106815800-106818000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr4:106815800-106818200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr4:106815800-106818600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr4:106815800-106818600	Active TSS	GM12878-XiMat	blood
14	chr4:106815800-106819200	Active TSS	Aorta	Aorta
15	chr4:106816000-106817400	Bivalent Enhancer	Stomach Mucosa	stomach
16	chr4:106816000-106817600	Bivalent/Poised TSS	HepG2	liver
17	chr4:106816000-106817800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:106816000-106817800	Bivalent Enhancer	Liver	Liver
19	chr4:106816000-106817800	Active TSS	Brain Substantia Nigra	brain
20	chr4:106816000-106817800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
21	chr4:106816000-106818000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr4:106816000-106818000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr4:106816000-106818000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:106816000-106818000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:106816000-106818000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:106816000-106818000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr4:106816000-106818000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:106816000-106818000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:106816000-106818000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:106816000-106818000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
31	chr4:106816000-106818000	Active TSS	Esophagus	oesophagus
32	chr4:106816000-106818000	Active TSS	Lung	lung
33	chr4:106816000-106818000	Active TSS	Psoas Muscle	Psoas
34	chr4:106816000-106818000	Active TSS	Right Atrium	heart
35	chr4:106816000-106818200	Active TSS	Fetal Heart	heart
36	chr4:106816000-106818200	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr4:106816000-106818800	Active TSS	Fetal Intestine Small	intestine
38	chr4:106816200-106817400	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr4:106816200-106817400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:106816200-106817400	Active TSS	Brain Cingulate Gyrus	brain
41	chr4:106816200-106817400	Active TSS	Fetal Lung	lung
42	chr4:106816200-106817400	Active TSS	Left Ventricle	heart
43	chr4:106816200-106817600	Bivalent/Poised TSS	Small Intestine	intestine
44	chr4:106816200-106817600	Bivalent/Poised TSS	A549	lung
45	chr4:106816200-106817600	Bivalent/Poised TSS	NHLF	lung
46	chr4:106816200-106817800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:106816200-106817800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:106816200-106817800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:106816200-106817800	Active TSS	Placenta Amnion	Placenta Amnion
50	chr4:106816200-106817800	Flanking Bivalent TSS/Enh	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links