Variant report

Variant	rs11658477
Chromosome Location	chr17:18044893-18044894
allele	A/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	RFX5	chr17:18044415-18044974	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr17:18044550-18044925	GM12878	blood:	n/a	n/a
3	CTCF	chr17:18044468-18044997	MCF-7	breast:	n/a	n/a
4	RAD21	chr17:18044441-18044954	A549	lung:	n/a	chr17:18044886-18044896
5	RAD21	chr17:18044520-18044934	SK-N-SH_RA	brain:	n/a	chr17:18044886-18044896
6	CTCF	chr17:18044760-18044910	WI-38	lung:	n/a	n/a
7	RAD21	chr17:18044480-18045115	HCT-116	colon:	n/a	chr17:18044886-18044896
8	RAD21	chr17:18044540-18044996	H1-hESC	embryonic stem cell:	n/a	chr17:18044886-18044896
9	RAD21	chr17:18044375-18045081	HCT-116	colon:	n/a	chr17:18044886-18044896
10	POLR2A	chr17:18044496-18044915	MCF10A-Er-Src	breast:	n/a	n/a
11	SMC3	chr17:18044444-18044910	HepG2	liver:	n/a	n/a
12	RAD21	chr17:18044472-18044996	ECC-1	luminal epithelium:	n/a	chr17:18044886-18044896
13	CTCF	chr17:18044310-18045055	HCT-116	colon:	n/a	n/a
14	RCOR1	chr17:18044550-18044895	K562	blood:	n/a	n/a
15	ZNF143	chr17:18044563-18044916	K562	blood:	n/a	n/a
16	RAD21	chr17:18044396-18045030	IMR90	lung:	n/a	chr17:18044886-18044896
17	MAZ	chr17:18044746-18044925	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr17:18044446-18044958	A549	lung:	n/a	n/a
19	RAD21	chr17:18044449-18044953	GM12878	blood:	n/a	chr17:18044886-18044896
20	CTCF	chr17:18044282-18044941	IMR90	lung:	n/a	n/a
21	SMC3	chr17:18044507-18044941	K562	blood:	n/a	n/a
22	CTCF	chr17:18044529-18044911	A549	lung:	n/a	n/a
23	CTCF	chr17:18044880-18045030	HFF-Myc	foreskin:	n/a	n/a
24	FOS	chr17:18044565-18044914	MCF10A-Er-Src	breast:	n/a	n/a
25	RAD21	chr17:18044497-18045024	A549	lung:	n/a	chr17:18044886-18044896
26	RAD21	chr17:18044458-18045031	ECC-1	luminal epithelium:	n/a	chr17:18044886-18044896
27	RAD21	chr17:18044495-18044921	HepG2	liver:	n/a	chr17:18044886-18044896
28	CTCF	chr17:18043985-18045480	A549	lung:	n/a	chr17:18045281-18045294
29	MYC	chr17:18044511-18044915	MCF10A-Er-Src	breast:	n/a	n/a
30	MAZ	chr17:18044541-18044959	K562	blood:	n/a	n/a
31	RAD21	chr17:18044562-18044948	HepG2	liver:	n/a	chr17:18044886-18044896
32	CTCF	chr17:18044329-18044931	GM12878	blood:	n/a	n/a
33	CTCF	chr17:18044820-18044970	HAc	cerebellar:	n/a	n/a
34	RAD21	chr17:18044613-18044989	MCF-7	breast:	n/a	chr17:18044886-18044896
35	POLR2A	chr17:18044486-18044998	MCF10A-Er-Src	breast:	n/a	n/a
36	RAD21	chr17:18044550-18044944	Hela-S3	cervix:	n/a	chr17:18044886-18044896
37	RAD21	chr17:18044425-18045004	MCF-7	breast:	n/a	chr17:18044886-18044896
38	RAD21	chr17:18044563-18044914	A549	lung:	n/a	chr17:18044886-18044896
39	ELK1	chr17:18044527-18045179	Hela-S3	cervix:	n/a	n/a
40	ARID3A	chr17:18044390-18044917	K562	blood:	n/a	n/a
41	CTCF	chr17:18044760-18044910	A549	lung:	n/a	n/a
42	CUX1	chr17:18044590-18045000	K562	blood:	n/a	n/a
43	CTCF	chr17:18044614-18044964	Lung_OC	lung:	n/a	n/a
44	E2F4	chr17:18044571-18044893	MCF10A-Er-Src	breast:	n/a	n/a
45	CTCF	chr17:18044166-18045329	SK-N-SH	brain:	n/a	chr17:18045281-18045294
46	RAD21	chr17:18044562-18044893	H1-hESC	embryonic stem cell:	n/a	n/a
47	JUND	chr17:18044549-18044908	K562	blood:	n/a	n/a
48	RAD21	chr17:18044529-18044894	SK-N-SH_RA	brain:	n/a	n/a
49	RAD21	chr17:18044190-18045308	SK-N-SH	brain:	n/a	chr17:18044886-18044896 chr17:18045282-18045295
50	PAX5	chr17:18044862-18045116	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18044305..18045021-chr17:18059355..18060391,3	MCF-7	breast:
2	chr17:18044182..18045939-chr17:18050102..18052001,2	MCF-7	breast:
3	chr17:18039043..18041825-chr17:18043264..18046470,4	K562	blood:
4	chr17:18044857..18048212-chr17:18048916..18052109,4	MCF-7	breast:
5	chr17:18042115..18044970-chr17:18226720..18228381,2	MCF-7	breast:
6	chr17:18039531..18041825-chr17:18044151..18046470,2	K562	blood:
7	chr17:18044150..18045078-chr17:18059256..18060265,3	MCF-7	breast:
8	chr17:18044679..18047861-chr17:18085770..18088322,3	MCF-7	breast:
9	chr17:18044317..18045124-chr17:18086070..18086665,2	MCF-7	breast:

Variant related genes	Relation type
MYO15A	TF binding region
ENSG00000238691	TF binding region
ENSG00000238691	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000091536	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000267350	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10048161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10451244	0.87[EUR][1000 genomes]
rs11078411	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11078412	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11652964	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653988	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11654146	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11654177	0.86[EUR][1000 genomes]
rs11654741	0.87[EUR][1000 genomes]
rs11655588	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs11655731	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11655797	0.87[EUR][1000 genomes]
rs11656035	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11657194	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11868832	0.84[EUR][1000 genomes]
rs11868886	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11869582	0.87[CEU][hapmap]
rs11871039	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11871491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs12449313	0.93[GIH][hapmap]
rs12600694	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13284	0.88[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs1563371	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1563373	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs16960980	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16960983	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs16960986	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs16960990	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs16960996	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs16961153	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs2015336	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2071242	0.96[GIH][hapmap];0.82[TSI][hapmap]
rs2290502	0.96[GIH][hapmap];0.84[TSI][hapmap]
rs2290503	0.96[GIH][hapmap];0.84[TSI][hapmap]
rs2294913	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs28364628	0.96[GIH][hapmap]
rs28811342	0.86[EUR][1000 genomes]
rs3088233	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs34474249	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36058389	0.86[EUR][1000 genomes]
rs3817992	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs3829956	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs55918833	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58441148	0.87[EUR][1000 genomes]
rs59354912	0.89[EUR][1000 genomes]
rs60285171	0.85[EUR][1000 genomes]
rs62072464	0.86[EUR][1000 genomes]
rs62072465	0.87[EUR][1000 genomes]
rs62072466	0.86[EUR][1000 genomes]
rs62072467	0.89[EUR][1000 genomes]
rs62072468	0.85[EUR][1000 genomes]
rs62072496	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072497	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62072498	0.87[EUR][1000 genomes]
rs62072500	0.87[EUR][1000 genomes]
rs62073602	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073603	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62073604	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62073605	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62073606	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62073607	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62073608	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62073609	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62073611	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62073615	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073649	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62073650	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6502640	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs7207276	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7215678	0.96[GIH][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs735960	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7498	0.96[GIH][hapmap];0.84[TSI][hapmap]
rs8065026	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8069094	0.90[EUR][1000 genomes]
rs8077577	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9913139	0.96[GIH][hapmap]
rs9916193	0.94[EUR][1000 genomes]
rs997315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv457697	chr17:18003845-18046290	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv574527	chr17:18003845-18046290	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
11	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv470580	chr17:18029857-18060192	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
13	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
14	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11658477	LOC162632	cis	parietal	SCAN
rs11658477	SHMT1	cis	cerebellum	SCAN
rs11658477	FLII	cis	cerebellum	SCAN
rs11658477	LOC162632	cis	cerebellum	SCAN
rs11658477	TRPV2	cis	cerebellum	SCAN
rs11658477	SLC47A1	cis	cerebellum	SCAN
rs11658477	PLD6	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18039600-18046800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr17:18039800-18046200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:18040600-18056000	Weak transcription	Gastric	stomach
4	chr17:18040800-18056400	Weak transcription	Right Atrium	heart
5	chr17:18041600-18045000	Enhancers	Placenta	Placenta
6	chr17:18043000-18045000	Enhancers	Fetal Muscle Trunk	muscle
7	chr17:18043400-18045200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:18043400-18046200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr17:18043600-18046800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:18044000-18045000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:18044000-18046000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:18044200-18045000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr17:18044200-18045400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
14	chr17:18044400-18045000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:18044400-18045000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr17:18044400-18045000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:18044400-18045000	Enhancers	Brain Angular Gyrus	brain
18	chr17:18044400-18045000	Enhancers	Colon Smooth Muscle	Colon
19	chr17:18044400-18045000	Enhancers	Fetal Intestine Small	intestine
20	chr17:18044400-18045000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
21	chr17:18044400-18045000	Enhancers	K562	blood
22	chr17:18044400-18045200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr17:18044400-18045200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr17:18044600-18045000	Weak transcription	Esophagus	oesophagus
25	chr17:18044600-18045000	Enhancers	GM12878-XiMat	blood
26	chr17:18044600-18045200	Enhancers	Brain Cingulate Gyrus	brain
27	chr17:18044600-18046400	Weak transcription	Pancreas	Pancrea
28	chr17:18044600-18046400	Weak transcription	HepG2	liver
29	chr17:18044600-18052200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:18044600-18053600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr17:18044800-18045000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:18044800-18047200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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