Variant report

Variant	rs6512916
Chromosome Location	chr20:52421497-52421498
allele	A/G/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	GATA3	chr20:52421227-52423123	A549	lung:	n/a	chr20:52421880-52421893
2	FOSL2	chr20:52421068-52424213	MCF-7	breast:	n/a	chr20:52421714-52421721
3	BCL3	chr20:52421386-52422856	A549	lung:	n/a	chr20:52422571-52422580
4	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
5	CEBPB	chr20:52421080-52424023	MCF-7	breast:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
6	CEBPB	chr20:52421283-52423021	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
7	CEBPB	chr20:52421398-52422316	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
8	RAD21	chr20:52421093-52424019	MCF-7	breast:	n/a	n/a
9	TCF12	chr20:52421349-52423181	A549	lung:	n/a	chr20:52421937-52421945
10	SP1	chr20:52421348-52423030	A549	lung:	n/a	chr20:52422052-52422061
11	BCL3	chr20:52421318-52422921	A549	lung:	n/a	chr20:52422571-52422580
12	HDAC2	chr20:52421104-52423988	MCF-7	breast:	n/a	chr20:52421328-52421337
13	EP300	chr20:52421270-52423029	A549	lung:	n/a	n/a
14	MEF2A	chr20:52421457-52422831	SK-N-SH	brain:	n/a	n/a
15	EP300	chr20:52421212-52423038	A549	lung:	n/a	n/a
16	SP1	chr20:52421283-52423043	A549	lung:	n/a	chr20:52422052-52422061
17	TEAD4	chr20:52421123-52423016	A549	lung:	n/a	n/a
18	HA-E2F1	chr20:52421201-52422903	MCF-7	breast:	n/a	n/a
19	TCF12	chr20:52421471-52422193	A549	lung:	n/a	chr20:52421937-52421945
20	MAX	chr20:52421354-52422980	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:57915032..57917929-chr20:52420971..52423307,2	MCF-7	breast:
2	chr10:135185314..135187385-chr20:52421033..52423723,2	MCF-7	breast:
3	chr20:52421177..52423554-chr3:62307174..62309545,2	MCF-7	breast:
4	chr20:52420212..52422332-chr4:120132097..120135086,2	MCF-7	breast:
5	chr17:56755338..56757573-chr20:52419856..52422679,2	MCF-7	breast:
6	chr1:149859688..149862015-chr20:52420095..52422543,2	MCF-7	breast:
7	chr20:52419455..52422452-chr20:55824806..55826636,2	MCF-7	breast:
8	chr20:52420462..52422354-chr20:59969368..59971665,2	MCF-7	breast:
9	chr20:52195072..52195578-chr20:52421449..52422396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225563	TF binding region
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000127884	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2904374	0.82[ASN][1000 genomes]
rs4491782	0.84[ASN][1000 genomes]
rs4811470	0.82[ASN][1000 genomes]
rs6126974	0.83[ASN][1000 genomes]
rs6126975	0.83[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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52412200-52421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:52414000-52421800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr20:52416000-52425600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52418000-52423400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr20:52418200-52421600	Enhancers	A549	lung
6	chr20:52418400-52422600	Enhancers	HepG2	liver
7	chr20:52418400-52422800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr20:52418600-52422400	Weak transcription	Fetal Intestine Small	intestine
9	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
10	chr20:52418800-52421800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr20:52419600-52421600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:52419600-52425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr20:52421400-52422600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:52421400-52423000	Enhancers	Osteobl	bone
15	chr20:52421400-52423600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr20:52421400-52423600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr20:52421400-52423600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:52421400-52423800	Enhancers	NHDF-Ad	bronchial
19	chr20:52421400-52423800	Enhancers	NHEK	skin
20	chr20:52421400-52424000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr20:52421400-52424000	Enhancers	HMEC	breast

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