Variant report

Variant	rs4656285
Chromosome Location	chr1:161043735-161043736
allele	A/C
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	chr1:161043533-161043889	HepG2	liver:	n/a	chr1:161043722-161043732 chr1:161043722-161043734 chr1:161043716-161043730
2	CTCF	chr1:161043600-161043750	Hela-S3	cervix:	n/a	chr1:161043719-161043732
3	MYC	chr1:161043559-161043947	MCF10A-Er-Src	breast:	n/a	chr1:161043785-161043795
4	POLR2A	chr1:161043399-161043927	HepG2	liver:	n/a	n/a
5	HMGN3	chr1:161043594-161043832	K562	blood:	n/a	n/a
6	SMC3	chr1:161043625-161043810	Hela-S3	cervix:	n/a	chr1:161043718-161043732
7	CTCF	chr1:161043640-161043790	GM12875	blood:	n/a	chr1:161043719-161043732
8	CTCF	chr1:161043700-161043850	GM12878	blood:	n/a	chr1:161043719-161043732
9	CTCF	chr1:161043700-161043850	GM12872	blood:	n/a	chr1:161043719-161043732
10	CTCF	chr1:161043680-161043830	HEK293	kidney:	n/a	chr1:161043719-161043732
11	HEY1	chr1:161043374-161043741	HepG2	liver:	n/a	n/a
12	CTCF	chr1:161043647-161043798	H1-hESC	embryonic stem cell:	n/a	chr1:161043719-161043732
13	SMC3	chr1:161043683-161043886	HepG2	liver:	n/a	chr1:161043718-161043732
14	CTCF	chr1:161043600-161043750	NHEK	skin:	n/a	chr1:161043719-161043732
15	CTCF	chr1:161043656-161043783	HepG2	liver:	n/a	chr1:161043719-161043732
16	CTCF	chr1:161043620-161043770	Caco-2	colon:	n/a	chr1:161043719-161043732
17	POLR2A	chr1:161043615-161043781	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:161043680-161043830	HMEC	breast:	n/a	chr1:161043719-161043732
19	CTCF	chr1:161043660-161043810	GM12872	blood:	n/a	chr1:161043719-161043732
20	CTCF	chr1:161043660-161043810	SAEC	small airway:	n/a	chr1:161043719-161043732
21	CTCF	chr1:161043700-161043850	GM12874	blood:	n/a	chr1:161043719-161043732
22	ZNF263	chr1:161043512-161044021	HEK293-T-REx	kidney:	n/a	n/a
23	CTCF	chr1:161043640-161043790	Caco-2	colon:	n/a	chr1:161043719-161043732
24	CTCF	chr1:161043680-161043830	GM12873	blood:	n/a	chr1:161043719-161043732
25	CTCF	chr1:161043582-161043855	GM12878	blood:	n/a	chr1:161043719-161043732
26	CTCF	chr1:161043640-161043790	WERI-Rb-1	eye:	n/a	chr1:161043719-161043732
27	MXI1	chr1:161043497-161043840	HepG2	liver:	n/a	n/a
28	MYC	chr1:161043683-161043764	MCF-7	breast:	n/a	n/a
29	MYC	chr1:161043616-161043854	MCF-7	breast:	n/a	chr1:161043785-161043795
30	CTCF	chr1:161043700-161043850	NHEK	skin:	n/a	chr1:161043719-161043732
31	RAD21	chr1:161043602-161043870	HepG2	liver:	n/a	chr1:161043722-161043732 chr1:161043722-161043734 chr1:161043716-161043730
32	CTCF	chr1:161043685-161043780	A549	lung:	n/a	chr1:161043719-161043732
33	CTCF	chr1:161043592-161043841	MCF-7	breast:	n/a	chr1:161043719-161043732
34	CTCF	chr1:161043684-161043751	LNCaP	prostate:	n/a	chr1:161043719-161043732
35	CTCF	chr1:161043640-161043790	HBMEC	blood vessel:	n/a	chr1:161043719-161043732
36	CTCF	chr1:161043665-161043780	ProgFib	skin:	n/a	chr1:161043719-161043732
37	CTCF	chr1:161043645-161043787	K562	blood:	n/a	chr1:161043719-161043732
38	MYC	chr1:161043532-161043890	MCF-7	breast:	n/a	chr1:161043785-161043795
39	FOS	chr1:161043646-161043774	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr1:161043623-161043815	MCF10A-Er-Src	breast:	n/a	n/a
41	RAD21	chr1:161043595-161043827	H1-hESC	embryonic stem cell:	n/a	chr1:161043722-161043732 chr1:161043722-161043734 chr1:161043716-161043730
42	CTCF	chr1:161043653-161043795	GM12878	blood:	n/a	chr1:161043719-161043732
43	CTCF	chr1:161043600-161043750	GM12864	blood:	n/a	chr1:161043719-161043732
44	MYC	chr1:161043521-161043949	MCF10A-Er-Src	breast:	n/a	chr1:161043785-161043795
45	CTCF	chr1:161043632-161043827	GM19239	blood:	n/a	chr1:161043719-161043732
46	FOS	chr1:161043666-161043796	MCF10A-Er-Src	breast:	n/a	n/a
47	CTCF	chr1:161043680-161043830	HepG2	liver:	n/a	chr1:161043719-161043732
48	CTCF	chr1:161043579-161043812	HepG2	liver:	n/a	chr1:161043719-161043732
49	CTCF	chr1:161043623-161043833	GM12892	blood:	n/a	chr1:161043719-161043732
50	RAD21	chr1:161043648-161043780	GM12878	blood:	n/a	chr1:161043722-161043732 chr1:161043722-161043734 chr1:161043716-161043730

No.	Distal block	Cell Line	Cell type
1	chr1:161039261..161041594-chr1:161042293..161044565,2	MCF-7	breast:
2	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
3	chr1:161040956..161045180-chr1:161134527..161136918,3	MCF-7	breast:
4	chr1:161037367..161040150-chr1:161043095..161044825,3	MCF-7	breast:
5	chr1:161006354..161009878-chr1:161042497..161045575,4	MCF-7	breast:

Variant related genes	Relation type
ARHGAP30	TF binding region
ENSG00000158773	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000143224	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000186517	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10908822	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265547	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265549	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs12142854	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12401309	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs1467742	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs1556257	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820097	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs3892376	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs4233364	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4656978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6671492	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv947135	chr1:161041002-161050287	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656285	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161030000-161046200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:161039600-161049000	Weak transcription	Lung	lung
3	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
4	chr1:161039800-161049000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:161039800-161052600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:161039800-161053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:161040000-161044400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:161040200-161045000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr1:161040200-161052600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:161040200-161052800	Weak transcription	Colonic Mucosa	Colon
11	chr1:161040800-161046800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:161041800-161043800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:161042000-161044200	Weak transcription	Pancreas	Pancrea
14	chr1:161042000-161045000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:161042000-161045000	Genic enhancers	Esophagus	oesophagus
16	chr1:161042000-161045000	Strong transcription	Gastric	stomach
17	chr1:161042000-161045000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:161042200-161044400	Weak transcription	K562	blood
19	chr1:161042400-161049400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:161043000-161046800	Enhancers	HMEC	breast
21	chr1:161043200-161044400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:161043200-161044400	Enhancers	NHEK	skin
23	chr1:161043400-161043800	Enhancers	Spleen	Spleen
24	chr1:161043400-161044000	Flanking Bivalent TSS/Enh	HepG2	liver
25	chr1:161043400-161044200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:161043400-161044600	Active TSS	HSMM	muscle
27	chr1:161043400-161044800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:161043400-161045000	Genic enhancers	Stomach Mucosa	stomach
29	chr1:161043400-161047000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:161043600-161043800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:161043600-161044000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:161043600-161044000	Transcr. at gene 5' and 3'	Placenta	Placenta
33	chr1:161043600-161045400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:161043600-161052800	Weak transcription	H1 Cell Line	embryonic stem cell

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