Variant report

Variant	rs61643643
Chromosome Location	chr5:112540216-112540217
allele	C/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	RAD21	chr5:112540121-112540530	SK-N-SH_RA	brain:	n/a	n/a
2	CEBPB	chr5:112540204-112540580	HepG2	liver:	n/a	chr5:112540384-112540397 chr5:112540385-112540396 chr5:112540384-112540395
3	POLR2A	chr5:112540127-112540564	U87	brain:	n/a	n/a
4	MXI1	chr5:112537418-112540905	SK-N-SH	brain:	n/a	n/a
5	CEBPB	chr5:112540210-112540597	Hela-S3	cervix:	n/a	chr5:112540384-112540397 chr5:112540385-112540396 chr5:112540384-112540395
6	REST	chr5:112540211-112540474	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr5:112540171-112540469	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr5:112540115-112540450	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr5:112540101-112540565	SK-N-MC	brain:	n/a	n/a
10	EP300	chr5:112540198-112540552	SK-N-SH_RA	brain:	n/a	n/a
11	CEBPB	chr5:112540199-112540610	ECC-1	luminal epithelium:	n/a	chr5:112540384-112540397 chr5:112540385-112540396 chr5:112540384-112540395
12	EP300	chr5:112538047-112541128	SK-N-SH	brain:	n/a	chr5:112540678-112540691
13	CEBPB	chr5:112540211-112540547	HepG2	liver:	n/a	chr5:112540384-112540397 chr5:112540385-112540396 chr5:112540384-112540395
14	CEBPB	chr5:112540215-112540571	IMR90	lung:	n/a	chr5:112540384-112540397 chr5:112540385-112540396 chr5:112540384-112540395
15	MYC	chr5:112540205-112540567	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr5:112540204-112540492	SK-N-SH_RA	brain:	n/a	n/a
17	CEBPB	chr5:112540170-112540588	ECC-1	luminal epithelium:	n/a	chr5:112540384-112540397 chr5:112540385-112540396 chr5:112540384-112540395
18	STAT3	chr5:112540204-112540502	MCF10A-Er-Src	breast:	n/a	n/a
19	GATA2	chr5:112540162-112540565	SH-SY5Y	brain:	n/a	n/a
20	TFAP2C	chr5:112540164-112540522	Hela-S3	cervix:	n/a	n/a
21	RAD21	chr5:112540212-112540482	SK-N-SH_RA	brain:	n/a	n/a
22	YY1	chr5:112540206-112540535	SK-N-SH_RA	brain:	n/a	n/a
23	POLR2A	chr5:112540001-112540525	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112537173..112539985-chr5:112540177..112543162,2	K562	blood:
2	chr5:112538594..112540259-chr5:112848065..112850694,2	MCF-7	breast:

Variant related genes	Relation type
MCC	TF binding region
ENSG00000047188	Chromatin interaction
ENSG00000171444	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10035647	1.00[ASN][1000 genomes]
rs10037038	1.00[ASN][1000 genomes]
rs10069434	1.00[ASN][1000 genomes]
rs10076511	1.00[ASN][1000 genomes]
rs10519339	1.00[ASN][1000 genomes]
rs10519340	1.00[ASN][1000 genomes]
rs10519342	1.00[ASN][1000 genomes]
rs11241199	1.00[ASN][1000 genomes]
rs11951541	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11958840	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13362511	1.00[ASN][1000 genomes]
rs17135464	1.00[ASN][1000 genomes]
rs17135493	1.00[ASN][1000 genomes]
rs17135511	1.00[ASN][1000 genomes]
rs1968992	1.00[ASN][1000 genomes]
rs2091802	1.00[ASN][1000 genomes]
rs55967427	1.00[ASN][1000 genomes]
rs56104704	1.00[ASN][1000 genomes]
rs56410005	1.00[ASN][1000 genomes]
rs57002698	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57602920	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57696719	1.00[ASN][1000 genomes]
rs57948635	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58069204	1.00[ASN][1000 genomes]
rs58237028	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58879623	1.00[ASN][1000 genomes]
rs59101992	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59673184	1.00[ASN][1000 genomes]
rs59807191	1.00[ASN][1000 genomes]
rs60185446	1.00[ASN][1000 genomes]
rs60590719	1.00[ASN][1000 genomes]
rs60636636	1.00[ASN][1000 genomes]
rs60727695	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61623201	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs61692685	1.00[ASN][1000 genomes]
rs62374390	1.00[ASN][1000 genomes]
rs634261	1.00[ASN][1000 genomes]
rs6859436	1.00[ASN][1000 genomes]
rs6859619	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874561	1.00[ASN][1000 genomes]
rs6878329	1.00[ASN][1000 genomes]
rs6899178	1.00[ASN][1000 genomes]
rs73244736	1.00[ASN][1000 genomes]
rs73244737	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244738	1.00[ASN][1000 genomes]
rs73244740	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244742	1.00[ASN][1000 genomes]
rs73244743	1.00[ASN][1000 genomes]
rs73244754	1.00[ASN][1000 genomes]
rs73244755	1.00[ASN][1000 genomes]
rs73244756	1.00[ASN][1000 genomes]
rs73244763	1.00[ASN][1000 genomes]
rs73244764	1.00[ASN][1000 genomes]
rs73244773	1.00[ASN][1000 genomes]
rs73244797	1.00[ASN][1000 genomes]
rs73246617	1.00[ASN][1000 genomes]
rs7702837	1.00[ASN][1000 genomes]
rs7708947	1.00[ASN][1000 genomes]
rs7710138	1.00[ASN][1000 genomes]
rs7723474	1.00[ASN][1000 genomes]
rs9326885	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112522600-112541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:112531800-112541000	Weak transcription	Aorta	Aorta
3	chr5:112533800-112541400	Weak transcription	Spleen	Spleen
4	chr5:112535600-112540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:112535600-112540600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:112535800-112540600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:112536400-112541800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:112537000-112540400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:112537200-112541800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr5:112537200-112542000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:112537400-112541200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:112537400-112541800	Enhancers	Adipose Nuclei	Adipose
13	chr5:112537600-112541200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:112538000-112541400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:112538400-112540400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:112538400-112541000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:112538400-112541200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:112538600-112540400	Flanking Active TSS	NHEK	skin
19	chr5:112538600-112541800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:112538600-112542000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:112538800-112541800	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:112538800-112542000	Enhancers	HMEC	breast
23	chr5:112538800-112544200	Weak transcription	Fetal Kidney	kidney
24	chr5:112539000-112541400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:112539000-112542000	Enhancers	Right Ventricle	heart
26	chr5:112539000-112547200	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:112539200-112540400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:112539200-112540600	Weak transcription	Placenta	Placenta
29	chr5:112539200-112540800	Enhancers	Brain Angular Gyrus	brain
30	chr5:112539200-112541000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:112539200-112541000	Enhancers	Hela-S3	cervix
32	chr5:112539200-112541200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr5:112539200-112541400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:112539200-112541600	Weak transcription	Gastric	stomach
35	chr5:112539200-112541600	Weak transcription	Lung	lung
36	chr5:112539200-112541800	Enhancers	Brain Hippocampus Middle	brain
37	chr5:112539200-112549200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:112539200-112554000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:112539400-112540400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:112539400-112540400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:112539400-112540400	Bivalent Enhancer	HepG2	liver
42	chr5:112539400-112541800	Flanking Active TSS	Liver	Liver
43	chr5:112539400-112541800	Enhancers	Fetal Lung	lung
44	chr5:112539400-112542000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:112539400-112542000	Enhancers	Right Atrium	heart
46	chr5:112539400-112542600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr5:112539400-112548000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr5:112539400-112548000	Weak transcription	Fetal Stomach	stomach
49	chr5:112539600-112540400	Enhancers	NHDF-Ad	bronchial
50	chr5:112539600-112544800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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