Variant report

Variant	rs4491782
Chromosome Location	chr20:52422481-52422482
allele	C/T
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	SIX5	chr20:52422416-52422717	A549	lung:	n/a	n/a
2	JUND	chr20:52422218-52422870	T-47D	breast:	n/a	n/a
3	POLR2A	chr20:52421606-52423054	PANC-1	pancreas:	n/a	n/a
4	FOXA1	chr20:52422315-52422807	T-47D	breast:	n/a	n/a
5	TCF7L2	chr20:52422335-52422856	PANC-1	pancreas:	n/a	n/a
6	TCF12	chr20:52422307-52422854	A549	lung:	n/a	n/a
7	GATA3	chr20:52421227-52423123	A549	lung:	n/a	chr20:52421880-52421893
8	ATF3	chr20:52421889-52422818	A549	lung:	n/a	n/a
9	FOS	chr20:52422371-52422871	MCF10A-Er-Src	breast:	n/a	chr20:52422570-52422581
10	REST	chr20:52422388-52422715	A549	lung:	n/a	chr20:52422474-52422483
11	GATA3	chr20:52422279-52422868	SK-N-SH	brain:	n/a	n/a
12	JUND	chr20:52422394-52422749	Hela-S3	cervix:	n/a	n/a
13	FOSL2	chr20:52421747-52423171	A549	lung:	n/a	n/a
14	TFAP2C	chr20:52422138-52422699	Hela-S3	cervix:	n/a	chr20:52422502-52422517
15	FOSL2	chr20:52422302-52422809	A549	lung:	n/a	n/a
16	GATA3	chr20:52422356-52422811	A549	lung:	n/a	n/a
17	FOSL2	chr20:52421068-52424213	MCF-7	breast:	n/a	chr20:52421714-52421721
18	JUN	chr20:52422383-52422753	Hela-S3	cervix:	n/a	n/a
19	BCL3	chr20:52421386-52422856	A549	lung:	n/a	chr20:52422571-52422580
20	GATA3	chr20:52382375-52424040	MCF-7	breast:	n/a	chr20:52402962-52402972 chr20:52418186-52418199 chr20:52417331-52417341 chr20:52405875-52405886 chr20:52403004-52403017 chr20:52421880-52421893 chr20:52384153-52384164 chr20:52391534-52391543 chr20:52409293-52409303 chr20:52391531-52391541 chr20:52385697-52385704 chr20:52417580-52417596 chr20:52417582-52417594 chr20:52384385-52384394
21	TEAD4	chr20:52421747-52422968	A549	lung:	n/a	n/a
22	RAD21	chr20:52421763-52422882	A549	lung:	n/a	n/a
23	CEBPB	chr20:52421080-52424023	MCF-7	breast:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
24	REST	chr20:52422298-52422621	PANC-1	pancreas:	n/a	chr20:52422474-52422483
25	FOXA2	chr20:52422371-52423037	A549	lung:	n/a	n/a
26	FOS	chr20:52421876-52422921	MCF10A-Er-Src	breast:	n/a	chr20:52422570-52422581
27	TEAD4	chr20:52422235-52422780	SK-N-SH	brain:	n/a	n/a
28	CEBPB	chr20:52421508-52422857	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
29	MYC	chr20:52422392-52422926	MCF10A-Er-Src	breast:	n/a	n/a
30	CEBPB	chr20:52422389-52422728	IMR90	lung:	n/a	n/a
31	FOS	chr20:52422426-52422736	Hela-S3	cervix:	n/a	chr20:52422570-52422581
32	FOS	chr20:52421848-52422915	MCF10A-Er-Src	breast:	n/a	chr20:52422570-52422581
33	CEBPB	chr20:52421283-52423021	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
34	JUND	chr20:52422212-52422927	T-47D	breast:	n/a	n/a
35	JUND	chr20:52422298-52422762	HCT-116	colon:	n/a	n/a
36	POLR2A	chr20:52422259-52422843	MCF10A-Er-Src	breast:	n/a	n/a
37	CEBPB	chr20:52422396-52422707	Hela-S3	cervix:	n/a	n/a
38	YY1	chr20:52422375-52422657	A549	lung:	n/a	n/a
39	GABPA	chr20:52422311-52422774	A549	lung:	n/a	n/a
40	STAT3	chr20:52422451-52422716	MCF10A-Er-Src	breast:	n/a	chr20:52422572-52422581 chr20:52422571-52422580
41	GATA3	chr20:52422215-52422933	T-47D	breast:	n/a	n/a
42	ELF1	chr20:52422301-52422678	A549	lung:	n/a	n/a
43	FOS	chr20:52422359-52422820	MCF10A-Er-Src	breast:	n/a	chr20:52422570-52422581
44	JUND	chr20:52422371-52422749	A549	lung:	n/a	n/a
45	RAD21	chr20:52421093-52424019	MCF-7	breast:	n/a	n/a
46	FOXA1	chr20:52422282-52422823	T-47D	breast:	n/a	n/a
47	ATF3	chr20:52422257-52422799	A549	lung:	n/a	n/a
48	NFIC	chr20:52422204-52422785	SK-N-SH	brain:	n/a	n/a
49	JUND	chr20:52422269-52422800	SK-N-SH	brain:	n/a	n/a
50	CEBPB	chr20:52422317-52422884	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:45987833..45989833-chr20:52422250..52425021,2	MCF-7	breast:
2	chr17:57915032..57917929-chr20:52420971..52423307,2	MCF-7	breast:
3	chr20:52422029..52422979-chr20:52483068..52483697,2	MCF-7	breast:
4	chr10:135185314..135187385-chr20:52421033..52423723,2	MCF-7	breast:
5	chr20:52390560..52391108-chr20:52422053..52422573,2	MCF-7	breast:
6	chr20:52422157..52422923-chr20:52486273..52486879,2	MCF-7	breast:
7	chr20:52421177..52423554-chr3:62307174..62309545,2	MCF-7	breast:
8	chr20:52404288..52406884-chr20:52421776..52423435,2	K562	blood:
9	chr20:52422353..52424027-chr5:1517557..1520340,2	MCF-7	breast:
10	chr17:57914402..57919000-chr20:52421915..52427149,7	MCF-7	breast:
11	chr17:56755338..56757573-chr20:52419856..52422679,2	MCF-7	breast:
12	chr17:57922372..57924896-chr20:52421508..52424076,4	MCF-7	breast:
13	chr20:52278376..52279004-chr20:52422159..52422813,2	MCF-7	breast:
14	chr1:149859688..149862015-chr20:52420095..52422543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225563	TF binding region
ENSG00000200997	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000127884	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11086441	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2191395	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2215401	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2215403	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2904374	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4809939	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4811470	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4811471	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4811472	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4811473	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4811474	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022757	0.81[AMR][1000 genomes]
rs6022761	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022762	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022763	0.82[AMR][1000 genomes]
rs6022764	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022766	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022767	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022768	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022769	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6022771	0.82[AMR][1000 genomes]
rs6091748	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6097585	0.86[ASN][1000 genomes]
rs6126974	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6126975	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62208456	0.86[AMR][1000 genomes]
rs6512916	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52416000-52425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:52418000-52423400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr20:52418400-52422600	Enhancers	HepG2	liver
4	chr20:52418400-52422800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
6	chr20:52419600-52425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:52421400-52422600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:52421400-52423000	Enhancers	Osteobl	bone
9	chr20:52421400-52423600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:52421400-52423600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr20:52421400-52423600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr20:52421400-52423800	Enhancers	NHDF-Ad	bronchial
13	chr20:52421400-52423800	Enhancers	NHEK	skin
14	chr20:52421400-52424000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:52421400-52424000	Enhancers	HMEC	breast
16	chr20:52421600-52422600	Flanking Active TSS	A549	lung
17	chr20:52421600-52422600	Enhancers	HSMM	muscle
18	chr20:52421600-52422600	Enhancers	NH-A	brain
19	chr20:52421600-52422800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr20:52421600-52422800	Enhancers	HUVEC	blood vessel
21	chr20:52421600-52423400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:52421600-52423800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr20:52421600-52423800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr20:52421600-52423800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:52421800-52422600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr20:52421800-52422600	Enhancers	HSMMtube	muscle
27	chr20:52421800-52422800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr20:52421800-52423000	Enhancers	Placenta	Placenta
29	chr20:52421800-52423800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:52421800-52423800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr20:52421800-52423800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr20:52421800-52423800	Enhancers	NHLF	lung
33	chr20:52422000-52425400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr20:52422000-52425800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:52422200-52422600	Flanking Active TSS	Hela-S3	cervix
36	chr20:52422200-52425800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr20:52422200-52425800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr20:52422200-52425800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr20:52422400-52422600	Enhancers	Fetal Intestine Small	intestine

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