Variant report

Variant	rs2089648
Chromosome Location	chr11:119512770-119512771
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	RAD21	chr11:119512709-119513125	H1-hESC	embryonic stem cell:	n/a	chr11:119512916-119512935
2	SMC3	chr11:119512759-119513111	GM12878	blood:	n/a	chr11:119512917-119512931
3	CTCF	chr11:119512734-119513112	K562	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
4	CTCF	chr11:119512760-119513055	GM12878	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
5	RAD21	chr11:119512650-119513279	SK-N-SH	brain:	n/a	chr11:119512916-119512935
6	RAD21	chr11:119512736-119513114	A549	lung:	n/a	chr11:119512916-119512935
7	CTCF	chr11:119512700-119512850	HA-sp	spinal cord:	n/a	n/a
8	RAD21	chr11:119512723-119513151	MCF-7	breast:	n/a	chr11:119512916-119512935
9	CTCF	chr11:119512670-119513050	K562	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
10	RAD21	chr11:119512745-119513127	HepG2	liver:	n/a	chr11:119512916-119512935
11	RAD21	chr11:119512762-119513140	GM12878	blood:	n/a	chr11:119512916-119512935
12	CTCF	chr11:119512762-119513002	Fibrobl	skin:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
13	RAD21	chr11:119512687-119513096	H1-hESC	embryonic stem cell:	n/a	chr11:119512916-119512935
14	SMC3	chr11:119512741-119513120	Hela-S3	cervix:	n/a	chr11:119512917-119512931
15	CTCF	chr11:119512763-119513060	GM19239	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
16	RAD21	chr11:119512698-119513206	ECC-1	luminal epithelium:	n/a	chr11:119512916-119512935
17	CTCF	chr11:119512704-119513083	GM12892	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
18	RAD21	chr11:119512741-119513159	ECC-1	luminal epithelium:	n/a	chr11:119512916-119512935
19	CTCF	chr11:119512710-119513134	HepG2	liver:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
20	RAD21	chr11:119512695-119513143	HepG2	liver:	n/a	chr11:119512916-119512935
21	CTCF	chr11:119512765-119513041	GM13977	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
22	ZNF143	chr11:119512761-119513031	K562	blood:	n/a	n/a
23	CTCF	chr11:119512720-119512870	HMEC	breast:	n/a	n/a
24	ZNF143	chr11:119512746-119513056	GM12878	blood:	n/a	n/a
25	CTCF	chr11:119512770-119513079	MCF-7	breast:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
26	CTCF	chr11:119512769-119513095	T-47D	breast:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
27	CTCF	chr11:119512745-119513094	IMR90	lung:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
28	CTCF	chr11:119512760-119513050	GM12864	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
29	CTCF	chr11:119512700-119512850	HFF	foreskin:	n/a	n/a
30	RAD21	chr11:119512755-119513096	IMR90	lung:	n/a	chr11:119512916-119512935
31	CTCF	chr11:119512700-119512850	HCM	heart:	n/a	n/a
32	CTCF	chr11:119512663-119513175	K562	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
33	CTCF	chr11:119512700-119512850	NHDF-neo	bronchial:	n/a	n/a
34	CTCF	chr11:119512722-119513080	GM12891	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
35	CTCF	chr11:119512725-119513026	K562	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
36	CTCF	chr11:119512700-119512850	HFF-Myc	foreskin:	n/a	n/a
37	RAD21	chr11:119512739-119513164	MCF-7	breast:	n/a	chr11:119512916-119512935
38	RAD21	chr11:119512754-119513114	Hela-S3	cervix:	n/a	chr11:119512916-119512935
39	CTCF	chr11:119512760-119512910	HL-60	blood:	n/a	n/a
40	RAD21	chr11:119512755-119513136	H1-hESC	embryonic stem cell:	n/a	chr11:119512916-119512935
41	CTCF	chr11:119512760-119512910	HAc	cerebellar:	n/a	n/a
42	CTCF	chr11:119512753-119513039	HepG2	liver:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
43	SMC3	chr11:119512765-119513107	K562	blood:	n/a	chr11:119512917-119512931
44	CTCF	chr11:119512761-119513036	GM10266	blood:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
45	RAD21	chr11:119512711-119513071	SK-N-SH_RA	brain:	n/a	chr11:119512916-119512935
46	CTCF	chr11:119512694-119513107	H1-hESC	embryonic stem cell:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
47	CTCF	chr11:119512700-119512850	GM12868	blood:	n/a	n/a
48	CTCF	chr11:119512652-119513226	HCT-116	colon:	n/a	chr11:119512917-119512938 chr11:119512918-119512931 chr11:119512918-119512927 chr11:119512916-119512932 chr11:119512915-119512933
49	SMC3	chr11:119512755-119513122	HepG2	liver:	n/a	chr11:119512917-119512931
50	CTCF	chr11:119512720-119512870	HCM	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:119512432..119513032-chr11:119599777..119600437,2	K562	blood:
2	chr11:119351973..119352705-chr11:119512520..119513396,3	MCF-7	breast:
3	chr11:119506334..119509273-chr11:119511344..119513114,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2523D13.1.1-2	chr11:119510206-119513699	ENSG00000254561.1

Variant related genes	Relation type
PVRL1	TF binding region
ENSG00000254854	Chromatin interaction
ENSG00000110400	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10892425	1.00[CEU][hapmap]
rs11217369	1.00[CEU][hapmap]
rs1546465	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2089646	0.85[CEU][hapmap]
rs4245199	0.85[CEU][hapmap]
rs4438048	0.85[CEU][hapmap]
rs4938699	0.85[CEU][hapmap]
rs4938700	1.00[CEU][hapmap]
rs7940667	0.85[CEU][hapmap]
rs906827	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042460	chr11:119430954-119540452	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv898419	chr11:119488646-119518006	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv898420	chr11:119488646-119541332	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv984471	chr11:119505802-119568473	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119510400-119513000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr11:119510600-119518400	Enhancers	Fetal Muscle Leg	muscle
3	chr11:119511200-119514400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:119511400-119517600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:119511600-119514400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:119511800-119513800	Weak transcription	Brain Germinal Matrix	brain
7	chr11:119512000-119513800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:119512200-119514200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:119512200-119514400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr11:119512600-119518800	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links