Variant report

Variant	rs2513658
Chromosome Location	chr11:66628249-66628250
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	ZNF263	chr11:66628209-66628511	HEK293-T-REx	kidney:	n/a	n/a
2	CTCF	chr11:66628180-66628330	HCPEpiC	choroid plexus:	n/a	n/a
3	POLR2A	chr11:66627956-66628596	A549	lung:	n/a	n/a
4	POLR2A	chr11:66628076-66628820	PFSK-1	brain:	n/a	n/a
5	CTCF	chr11:66628074-66628375	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:66627971-66628339	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr11:66628171-66628371	Hela-S3	cervix:	n/a	chr11:66628339-66628351
8	POLR2A	chr11:66628116-66628558	GM12878	blood:	n/a	n/a
9	POLR2A	chr11:66628192-66628300	A549	lung:	n/a	n/a
10	BCL3	chr11:66627702-66628541	A549	lung:	n/a	n/a
11	POLR2A	chr11:66626400-66629045	K562	blood:	n/a	n/a
12	POLR2A	chr11:66627943-66628467	A549	lung:	n/a	n/a
13	SMC3	chr11:66628055-66628388	Hela-S3	cervix:	n/a	n/a
14	RAD21	chr11:66627933-66628446	H1-hESC	embryonic stem cell:	n/a	chr11:66628339-66628351
15	CTCF	chr11:66628166-66628251	GM12891	blood:	n/a	n/a
16	POLR2A	chr11:66627958-66628550	HL-60	blood:	n/a	n/a
17	SMARCB1	chr11:66623203-66629011	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr11:66624704-66629085	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr11:66627815-66628530	H1-hESC	embryonic stem cell:	n/a	n/a
20	BCL3	chr11:66628088-66628668	A549	lung:	n/a	n/a
21	POLR2A	chr11:66627963-66629062	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr11:66628238-66628619	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr11:66623305-66630473	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr11:66628120-66628297	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr11:66628200-66628350	HEEpiC	esophagus:	n/a	n/a
26	MAX	chr11:66627967-66628463	H1-hESC	embryonic stem cell:	n/a	chr11:66628249-66628260 chr11:66628248-66628263
27	CTCF	chr11:66628155-66628279	NHEK	skin:	n/a	n/a
28	POLR2A	chr11:66628202-66629020	GM12892	blood:	n/a	n/a
29	CTCF	chr11:66628014-66628303	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr11:66628063-66628360	H1-hESC	embryonic stem cell:	n/a	chr11:66628339-66628351
31	POLR2A	chr11:66628066-66628632	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr11:66628124-66628335	HepG2	liver:	n/a	n/a
33	CTCF	chr11:66628150-66628272	MCF-7	breast:	n/a	n/a
34	CTCF	chr11:66628125-66628291	HepG2	liver:	n/a	n/a
35	JUND	chr11:66628009-66628303	A549	lung:	n/a	chr11:66628239-66628253
36	POLR2A	chr11:66626135-66629497	K562	blood:	n/a	n/a
37	POLR2A	chr11:66627953-66628500	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr11:66627915-66628891	PANC-1	pancreas:	n/a	n/a
39	MXI1	chr11:66628157-66628277	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr11:66627878-66629756	A549	lung:	n/a	n/a
41	POLR2A	chr11:66628048-66628676	GM12892	blood:	n/a	n/a
42	RAD21	chr11:66628124-66628344	SK-N-SH_RA	brain:	n/a	n/a
43	RAD21	chr11:66627949-66628494	A549	lung:	n/a	chr11:66628339-66628351
44	RAD21	chr11:66628058-66628400	H1-hESC	embryonic stem cell:	n/a	chr11:66628339-66628351
45	POLR2A	chr11:66623068-66630428	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr11:66628099-66628313	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr11:66623077-66631490	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr11:66627987-66628687	A549	lung:	n/a	n/a
49	CTCF	chr11:66628188-66628256	A549	lung:	n/a	n/a
50	MAX	chr11:66627913-66628447	A549	lung:	n/a	chr11:66628249-66628260 chr11:66628248-66628263

No.	Distal block	Cell Line	Cell type
1	chr11:66628190..66631041-chr11:66791870..66794073,2	MCF-7	breast:
2	chr11:66626403..66628670-chr11:67229720..67232252,2	K562	blood:
3	chr11:65624214..65625937-chr11:66627992..66630258,2	K562	blood:

Variant related genes	Relation type
PC	TF binding region
ENSG00000270169	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000172757	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12577111	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12805133	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2276138	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3741363	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs4930387	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4930391	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs508443	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs543191	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs551708	0.82[TSI][hapmap]
rs569818	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs594313	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs608248	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap]
rs627330	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682842	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7107944	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv508638	chr11:66541653-66643634	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	nsv897795	chr11:66608521-66637926	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2513658	SYT12	cis	parietal	SCAN
rs2513658	ACTN3	cis	Muscle Skeletal	GTEx
rs2513658	EHBP1L1	cis	cerebellum	SCAN
rs2513658	SNORA57	cis	cerebellum	SCAN
rs2513658	FGF4	cis	parietal	SCAN
rs2513658	CCS	cis	lymphoblastoid	seeQTL
rs2513658	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs2513658	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs2513658	KDM2A	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66624200-66645000	Weak transcription	Fetal Kidney	kidney
2	chr11:66624400-66630800	Weak transcription	NHEK	skin
3	chr11:66624400-66636000	Weak transcription	Primary T cells from cord blood	blood
4	chr11:66624400-66637400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr11:66624400-66640200	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:66624800-66637400	Weak transcription	Aorta	Aorta
7	chr11:66625000-66631200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:66625000-66636200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:66625000-66648800	Weak transcription	Right Atrium	heart
10	chr11:66625200-66628400	Weak transcription	NHDF-Ad	bronchial
11	chr11:66625200-66628800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:66625200-66631200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:66625400-66628400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:66625400-66628400	Genic enhancers	Adipose Nuclei	Adipose
15	chr11:66625400-66629400	Weak transcription	Brain Angular Gyrus	brain
16	chr11:66625400-66629600	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:66625400-66630800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:66625400-66631200	Weak transcription	Brain Anterior Caudate	brain
19	chr11:66625400-66631600	Weak transcription	HSMMtube	muscle
20	chr11:66625400-66632000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:66625400-66632200	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr11:66625400-66632800	Weak transcription	HepG2	liver
23	chr11:66625400-66634600	Strong transcription	Fetal Stomach	stomach
24	chr11:66625400-66636000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:66625400-66636000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:66625400-66642200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:66625400-66642200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:66625400-66645400	Weak transcription	Fetal Lung	lung
29	chr11:66625400-66645800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:66625400-66648000	Weak transcription	Left Ventricle	heart
31	chr11:66625400-66650600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:66625600-66628800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:66625600-66628800	Strong transcription	Thymus	Thymus
34	chr11:66625600-66629000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr11:66625600-66630200	Strong transcription	NHLF	lung
36	chr11:66625600-66631800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr11:66625600-66636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr11:66625600-66636200	Strong transcription	Fetal Intestine Small	intestine
39	chr11:66625800-66629000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:66625800-66630000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:66625800-66630200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:66625800-66630200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:66625800-66630400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr11:66625800-66636200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:66625800-66636400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:66625800-66650800	Weak transcription	Osteobl	bone
47	chr11:66626000-66628400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr11:66626000-66633600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:66626200-66628600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:66626200-66632000	Weak transcription	Fetal Heart	heart

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