Variant report

Variant	rs5218
Chromosome Location	chr11:17409069-17409070
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	CTCF	chr11:17408920-17409070	HBMEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17407664..17411994-chr11:17495609..17498712,4	MCF-7	breast:
2	chr11:17407926..17410738-chr11:17427633..17429679,2	MCF-7	breast:

Variant related genes	Relation type
KCNJ11	TF binding region
ENSG00000006071	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1002227	1.00[ASW][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10430892	0.91[CHB][hapmap]
rs10466382	1.00[ASW][hapmap]
rs10766383	1.00[ASW][hapmap]
rs10766384	1.00[ASW][hapmap]
rs10766385	0.82[ASW][hapmap]
rs10766389	1.00[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs10766390	0.87[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10766391	0.87[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10766392	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10766393	1.00[ASW][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10766396	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10832757	1.00[ASW][hapmap]
rs10832765	0.82[ASW][hapmap]
rs10832768	0.82[ASW][hapmap]
rs10832772	0.87[CHB][hapmap]
rs10832775	0.87[CHB][hapmap]
rs10832779	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10832781	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10832782	0.83[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs10832785	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs11024246	0.82[CHB][hapmap]
rs11024262	0.87[CHB][hapmap]
rs11024263	0.87[CHB][hapmap]
rs11024272	0.83[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs11024273	0.90[CEU][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs11024275	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2018218	0.83[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2067043	0.85[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2074312	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2074313	0.95[EUR][1000 genomes]
rs2079042	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2285676	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs2354867	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs34327804	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3741203	1.00[ASW][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41282912	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4148638	0.89[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4756887	0.83[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs71484767	0.80[EUR][1000 genomes]
rs886288	0.83[JPT][hapmap]
rs9633836	0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9645621	1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv467712	chr11:17393644-17418477	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv553583	chr11:17393644-17418477	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv517772	chr11:17401134-17427862	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv897018	chr11:17403639-17417337	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv528959	chr11:17403639-17435214	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv540951	chr11:17404438-17422755	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv482158	chr11:17406798-17410206	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv540952	chr11:17407913-17422755	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv467713	chr11:17408025-17440473	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv553584	chr11:17408025-17440473	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5218	NCR3LG1	cis	Esophagus Mucosa	GTEx
rs5218	RP1-239B22.5	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17394400-17410200	Weak transcription	A549	lung
2	chr11:17395200-17410200	Weak transcription	Thymus	Thymus
3	chr11:17395600-17410200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:17395600-17410400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:17395800-17409200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:17396600-17410200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:17398200-17410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:17398800-17410200	Weak transcription	Primary T cells from cord blood	blood
9	chr11:17400800-17410200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:17401000-17410200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:17401600-17410200	Weak transcription	Hela-S3	cervix
12	chr11:17401600-17410200	Weak transcription	K562	blood
13	chr11:17401800-17410200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr11:17402000-17410200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:17402000-17410200	Weak transcription	HMEC	breast
16	chr11:17403000-17410400	Weak transcription	Aorta	Aorta
17	chr11:17403800-17410400	Weak transcription	HSMMtube	muscle
18	chr11:17404200-17410200	Weak transcription	HSMM	muscle
19	chr11:17405200-17412000	Enhancers	Fetal Brain Male	brain
20	chr11:17405400-17409800	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr11:17405600-17409200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
22	chr11:17406000-17410200	Weak transcription	Brain Hippocampus Middle	brain
23	chr11:17407200-17410200	Enhancers	Lung	lung
24	chr11:17407800-17409200	Enhancers	GM12878-XiMat	blood
25	chr11:17407800-17410400	Enhancers	Fetal Heart	heart
26	chr11:17408000-17410200	Weak transcription	Right Atrium	heart
27	chr11:17408200-17409200	Weak transcription	Brain Anterior Caudate	brain
28	chr11:17408200-17409600	Genic enhancers	Pancreas	Pancrea
29	chr11:17408200-17410200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr11:17408200-17410200	Enhancers	Right Ventricle	heart
31	chr11:17408400-17409200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:17408400-17409600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:17408400-17409600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
34	chr11:17408400-17410200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:17408400-17410200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:17408400-17410200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr11:17408600-17409200	Strong transcription	Fetal Brain Female	brain
38	chr11:17408600-17409400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:17408600-17409400	Strong transcription	Fetal Intestine Small	intestine
40	chr11:17408600-17409800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:17408600-17410200	Weak transcription	Brain Angular Gyrus	brain
42	chr11:17408800-17409200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr11:17408800-17409200	ZNF genes & repeats	Brain Germinal Matrix	brain
44	chr11:17408800-17409200	ZNF genes & repeats	Esophagus	oesophagus
45	chr11:17408800-17409600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:17408800-17409600	Enhancers	Psoas Muscle	Psoas
47	chr11:17408800-17409800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:17409000-17409600	Strong transcription	Fetal Muscle Leg	muscle
49	chr11:17409000-17410200	Enhancers	Gastric	stomach
50	chr11:17409000-17410200	Weak transcription	Left Ventricle	heart

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