Variant report

Variant	rs6097587
Chromosome Location	chr20:52422016-52422017
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	POLR2A	chr20:52421606-52423054	PANC-1	pancreas:	n/a	n/a
2	GATA3	chr20:52421227-52423123	A549	lung:	n/a	chr20:52421880-52421893
3	ATF3	chr20:52421889-52422818	A549	lung:	n/a	n/a
4	FOSL2	chr20:52421747-52423171	A549	lung:	n/a	n/a
5	FOSL2	chr20:52421068-52424213	MCF-7	breast:	n/a	chr20:52421714-52421721
6	BCL3	chr20:52421386-52422856	A549	lung:	n/a	chr20:52422571-52422580
7	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
8	TEAD4	chr20:52421747-52422968	A549	lung:	n/a	n/a
9	RAD21	chr20:52421763-52422882	A549	lung:	n/a	n/a
10	CEBPB	chr20:52421080-52424023	MCF-7	breast:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
11	FOS	chr20:52421876-52422921	MCF10A-Er-Src	breast:	n/a	chr20:52422570-52422581
12	CTCF	chr20:52421920-52422070	AG04449	skin:	n/a	n/a
13	CEBPB	chr20:52421508-52422857	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
14	FOS	chr20:52421848-52422915	MCF10A-Er-Src	breast:	n/a	chr20:52422570-52422581
15	CEBPB	chr20:52421283-52423021	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
16	CEBPB	chr20:52421398-52422316	A549	lung:	n/a	chr20:52421706-52421717 chr20:52421627-52421638
17	STAT3	chr20:52421878-52422078	MCF10A-Er-Src	breast:	n/a	n/a
18	TCF7L2	chr20:52421739-52422128	PANC-1	pancreas:	n/a	n/a
19	RAD21	chr20:52421093-52424019	MCF-7	breast:	n/a	n/a
20	POLR2A	chr20:52421678-52422984	PANC-1	pancreas:	n/a	n/a
21	TCF12	chr20:52421349-52423181	A549	lung:	n/a	chr20:52421937-52421945
22	MYC	chr20:52421944-52422087	MCF10A-Er-Src	breast:	n/a	n/a
23	SP1	chr20:52421348-52423030	A549	lung:	n/a	chr20:52422052-52422061
24	REST	chr20:52421985-52422917	A549	lung:	n/a	chr20:52422474-52422483
25	BCL3	chr20:52421318-52422921	A549	lung:	n/a	chr20:52422571-52422580
26	FOS	chr20:52421879-52422149	MCF10A-Er-Src	breast:	n/a	n/a
27	CTCF	chr20:52421900-52422050	MCF-7	breast:	n/a	n/a
28	HDAC2	chr20:52421104-52423988	MCF-7	breast:	n/a	chr20:52421328-52421337
29	EP300	chr20:52421270-52423029	A549	lung:	n/a	n/a
30	POLR2A	chr20:52421771-52422227	ProgFib	skin:	n/a	n/a
31	SIN3AK20	chr20:52421966-52422735	A549	lung:	n/a	n/a
32	CTCF	chr20:52421900-52422050	HBMEC	blood vessel:	n/a	n/a
33	RCOR1	chr20:52421973-52422147	HepG2	liver:	n/a	n/a
34	MAX	chr20:52421611-52422935	A549	lung:	n/a	n/a
35	MEF2A	chr20:52421457-52422831	SK-N-SH	brain:	n/a	n/a
36	CTCF	chr20:52421900-52422050	AG04449	skin:	n/a	n/a
37	EP300	chr20:52421212-52423038	A549	lung:	n/a	n/a
38	SP1	chr20:52421283-52423043	A549	lung:	n/a	chr20:52422052-52422061
39	TEAD4	chr20:52421123-52423016	A549	lung:	n/a	n/a
40	HA-E2F1	chr20:52421201-52422903	MCF-7	breast:	n/a	n/a
41	EP300	chr20:52421937-52422047	HepG2	liver:	n/a	n/a
42	RAD21	chr20:52421894-52422087	HepG2	liver:	n/a	n/a
43	CTCF	chr20:52421920-52422070	HepG2	liver:	n/a	n/a
44	TCF12	chr20:52421471-52422193	A549	lung:	n/a	chr20:52421937-52421945
45	MAX	chr20:52421354-52422980	A549	lung:	n/a	n/a
46	SIX5	chr20:52421588-52422918	A549	lung:	n/a	n/a
47	SMC3	chr20:52421709-52422149	HepG2	liver:	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	chr20:52404288..52406884-chr20:52421776..52423435,2	K562	blood:
6	chr17:57914402..57919000-chr20:52421915..52427149,7	MCF-7	breast:
7	chr17:56755338..56757573-chr20:52419856..52422679,2	MCF-7	breast:
8	chr17:57922372..57924896-chr20:52421508..52424076,4	MCF-7	breast:
9	chr20:52421541..52422373-chr20:52765421..52765961,2	MCF-7	breast:
10	chr1:149859688..149862015-chr20:52420095..52422543,2	MCF-7	breast:
11	chr20:52419455..52422452-chr20:55824806..55826636,2	MCF-7	breast:
12	chr20:52420462..52422354-chr20:59969368..59971665,2	MCF-7	breast:
13	chr20:52195072..52195578-chr20:52421449..52422396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225563	TF binding region
ENSG00000145390	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000127884	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2870288	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4809937	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4811469	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4811470	0.82[JPT][hapmap]
rs6022774	0.81[AMR][1000 genomes]
rs6022781	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs6022783	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap]
rs7271143	0.88[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6097587	C20orf43	cis	cerebellum	SCAN

Chromatin state (count:40 , 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	chr20:52418600-52422400	Weak transcription	Fetal Intestine Small	intestine
6	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
7	chr20:52419600-52425600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:52421400-52422600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:52421400-52423000	Enhancers	Osteobl	bone
10	chr20:52421400-52423600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr20:52421400-52423600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr20:52421400-52423600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr20:52421400-52423800	Enhancers	NHDF-Ad	bronchial
14	chr20:52421400-52423800	Enhancers	NHEK	skin
15	chr20:52421400-52424000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr20:52421400-52424000	Enhancers	HMEC	breast
17	chr20:52421600-52422200	Enhancers	Hela-S3	cervix
18	chr20:52421600-52422600	Flanking Active TSS	A549	lung
19	chr20:52421600-52422600	Enhancers	HSMM	muscle
20	chr20:52421600-52422600	Enhancers	NH-A	brain
21	chr20:52421600-52422800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr20:52421600-52422800	Enhancers	HUVEC	blood vessel
23	chr20:52421600-52423400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:52421600-52423800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr20:52421600-52423800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr20:52421600-52423800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr20:52421800-52422200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr20:52421800-52422200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr20:52421800-52422200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr20:52421800-52422400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr20:52421800-52422600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr20:52421800-52422600	Enhancers	HSMMtube	muscle
33	chr20:52421800-52422800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:52421800-52423000	Enhancers	Placenta	Placenta
35	chr20:52421800-52423800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr20:52421800-52423800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr20:52421800-52423800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr20:52421800-52423800	Enhancers	NHLF	lung
39	chr20:52422000-52425400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr20:52422000-52425800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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