Variant report

Variant	rs979894
Chromosome Location	chr11:27061690-27061691
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	CTCF	chr11:27061620-27061770	A549	lung:	n/a	chr11:27061627-27061645
2	STAT3	chr11:27061657-27062636	MCF10A-Er-Src	breast:	n/a	chr11:27061795-27061803 chr11:27062471-27062479
3	CTCF	chr11:27061560-27061710	AG09309	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
4	RAD21	chr11:27061474-27061834	H1-hESC	embryonic stem cell:	n/a	chr11:27061628-27061647
5	CTCF	chr11:27061493-27061695	HepG2	liver:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
6	CTCF	chr11:27061542-27061698	ProgFib	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
7	CTCF	chr11:27061560-27061710	HRE	kidney:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
8	CTCF	chr11:27061536-27061697	MCF-7	breast:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
9	CTCF	chr11:27061580-27061730	HMEC	breast:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
10	CTCF	chr11:27061540-27061690	MCF-7	breast:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
11	CTCF	chr11:27061557-27061694	LNCaP	prostate:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
12	RAD21	chr11:27061504-27061762	SK-N-SH_RA	brain:	n/a	chr11:27061628-27061647
13	CTCF	chr11:27061583-27061698	Kidney_OC	kidney:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
14	CTCF	chr11:27061560-27061710	HPF	lung:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
15	CTCF	chr11:27061600-27061750	BJ	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
16	CTCF	chr11:27061560-27061710	SAEC	small airway:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
17	RAD21	chr11:27061475-27061826	H1-hESC	embryonic stem cell:	n/a	chr11:27061628-27061647
18	STAT3	chr11:27061670-27062922	MCF10A-Er-Src	breast:	n/a	chr11:27061795-27061803 chr11:27062471-27062479
19	RAD21	chr11:27061495-27061785	A549	lung:	n/a	chr11:27061628-27061647
20	POLR2A	chr11:27061536-27063509	MCF10A-Er-Src	breast:	n/a	n/a
21	CTCF	chr11:27061600-27061750	AG10803	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
22	CTCF	chr11:27061580-27061730	Hela-S3	cervix:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
23	STAT3	chr11:27061658-27063043	MCF10A-Er-Src	breast:	n/a	chr11:27061795-27061803 chr11:27062471-27062479
24	FOS	chr11:27061485-27062897	MCF10A-Er-Src	breast:	n/a	chr11:27061973-27061980 chr11:27061973-27061981 chr11:27061974-27061985 chr11:27061971-27061983
25	CTCF	chr11:27061580-27061730	HRPEpiC	eye:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
26	CTCF	chr11:27061640-27061790	HAc	cerebellar:	n/a	n/a
27	CTCF	chr11:27061580-27061730	BJ	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
28	CTCF	chr11:27061580-27061730	AG09319	gingival:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
29	CTCF	chr11:27061540-27061690	HBMEC	blood vessel:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
30	CTCF	chr11:27061580-27061730	SAEC	small airway:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
31	RAD21	chr11:27061480-27061738	HepG2	liver:	n/a	chr11:27061628-27061647
32	CTCF	chr11:27061600-27061750	HCPEpiC	choroid plexus:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
33	RAD21	chr11:27061499-27061708	SK-N-SH_RA	brain:	n/a	chr11:27061628-27061647
34	CTCF	chr11:27061620-27061770	NHDF-neo	bronchial:	n/a	chr11:27061627-27061645
35	CTCF	chr11:27061540-27061690	AG04449	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
36	CTCF	chr11:27061540-27061690	Caco-2	colon:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
37	CTCF	chr11:27061540-27061690	AG04450	lung:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
38	CTCF	chr11:27061620-27061770	K562	blood:	n/a	chr11:27061627-27061645
39	SMC3	chr11:27061493-27061795	HepG2	liver:	n/a	n/a
40	MYC	chr11:27061498-27062895	MCF10A-Er-Src	breast:	n/a	n/a
41	CTCF	chr11:27061441-27061785	H1-hESC	embryonic stem cell:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
42	CTCF	chr11:27061540-27061690	WERI-Rb-1	eye:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
43	CTCF	chr11:27061640-27061790	HFF-Myc	foreskin:	n/a	n/a
44	RAD21	chr11:27061402-27061803	HepG2	liver:	n/a	chr11:27061628-27061647
45	CTCF	chr11:27061556-27061714	HepG2	liver:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
46	RAD21	chr11:27061465-27061714	H1-hESC	embryonic stem cell:	n/a	chr11:27061628-27061647
47	CTCF	chr11:27061600-27061750	HFF	foreskin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
48	CTCF	chr11:27061580-27061730	AG04449	skin:	n/a	chr11:27061627-27061645 chr11:27061609-27061617
49	MYC	chr11:27061660-27062192	MCF10A-Er-Src	breast:	n/a	n/a
50	CTCF	chr11:27061580-27061730	HPAF	blood vessel:	n/a	chr11:27061627-27061645 chr11:27061609-27061617

Variant related genes	Relation type
BBOX1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10501074	0.82[ASN][1000 genomes]
rs10767592	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs10767593	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10767595	0.83[JPT][hapmap]
rs10835104	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835105	0.90[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10835108	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10835110	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835111	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11029793	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11029794	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11029805	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11029806	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11029810	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11029811	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11029817	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11029819	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11826702	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11828894	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12288789	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1442935	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1442936	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1445315	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1445317	0.83[JPT][hapmap]
rs1584011	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1596252	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1596253	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2083745	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2165771	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2165772	0.95[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2351062	0.82[ASN][1000 genomes]
rs2351063	0.82[ASN][1000 genomes]
rs28541300	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35248831	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4145909	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4923411	0.82[ASN][1000 genomes]
rs4923412	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4923419	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56240135	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58021263	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59096630	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60106088	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7119888	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7125612	0.82[ASN][1000 genomes]
rs7926675	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7926773	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7932626	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7936060	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs980804	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916187	chr11:26576875-27328603	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949332	chr11:26935972-27223492	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv897147	chr11:26983363-27258899	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1040964	chr11:26998213-27223388	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv540975	chr11:26998213-27223388	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv949575	chr11:27005687-27233359	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv533052	chr11:27006061-27225374	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv553912	chr11:27014032-27240951	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv467781	chr11:27019331-27240951	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv553913	chr11:27019331-27240951	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv897148	chr11:27026424-27071118	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv508619	chr11:27028494-27110734	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:27052000-27061800	Weak transcription	Aorta	Aorta
2	chr11:27054600-27062000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:27060600-27064000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:27061400-27063600	Enhancers	HMEC	breast
5	chr11:27061600-27061800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:27061600-27061800	Flanking Active TSS	NHEK	skin
7	chr11:27061600-27062400	Enhancers	Fetal Kidney	kidney
8	chr11:27061600-27063000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr11:27061600-27063200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr11:27061600-27063600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr11:27061600-27064000	Enhancers	Cortex derived primary cultured neurospheres	brain

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