Variant report

Variant	rs11211167
Chromosome Location	chr1:46162482-46162483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46152318..46155647-chr1:46160597..46165176,4	MCF-7	breast:
2	chr1:46161054..46163559-chr1:46163619..46166713,3	MCF-7	breast:
3	chr1:46151352..46155002-chr1:46160340..46164290,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPBP1L1-1	chr1:46162434-46162747	ENSG00000230896.1

Variant related genes	Relation type
ENSG00000197429	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000159596	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11211127	1.00[AMR][1000 genomes]
rs11211144	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211150	0.81[LWK][hapmap];0.91[MKK][hapmap]
rs11211153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12057167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12063380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12067882	1.00[AMR][1000 genomes]
rs12070146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073045	1.00[AMR][1000 genomes]
rs12073047	1.00[AMR][1000 genomes]
rs12077112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081121	1.00[AMR][1000 genomes]
rs12082672	1.00[AMR][1000 genomes]
rs12085372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086880	1.00[AMR][1000 genomes]
rs12088810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091335	1.00[AMR][1000 genomes]
rs12091360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093444	1.00[AMR][1000 genomes]
rs12094011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097914	1.00[AMR][1000 genomes]
rs16832550	1.00[AMR][1000 genomes]
rs16832553	1.00[AMR][1000 genomes]
rs16832557	1.00[AMR][1000 genomes]
rs1691225	1.00[AMR][1000 genomes]
rs1691226	1.00[AMR][1000 genomes]
rs1691227	1.00[AMR][1000 genomes]
rs1762087	1.00[AMR][1000 genomes]
rs2782489	1.00[AMR][1000 genomes]
rs28532613	1.00[AMR][1000 genomes]
rs28548585	1.00[AMR][1000 genomes]
rs28576912	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs28589341	1.00[CEU][hapmap]
rs28607905	1.00[AMR][1000 genomes]
rs35067820	1.00[AMR][1000 genomes]
rs35808563	1.00[AMR][1000 genomes]
rs486346	1.00[AMR][1000 genomes]
rs505175	0.92[MKK][hapmap];1.00[AMR][1000 genomes]
rs506094	1.00[AMR][1000 genomes]
rs525706	1.00[AMR][1000 genomes]
rs622296	1.00[AMR][1000 genomes]
rs635446	1.00[AMR][1000 genomes]
rs665014	1.00[AMR][1000 genomes]
rs668289	0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs669417	0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs680267	1.00[AMR][1000 genomes]
rs7550744	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
7	nsv1010054	chr1:46144479-46320493	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
8	nsv1006861	chr1:46144479-46417621	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	76 gene(s)	inside rSNPs	diseases
9	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
10	nsv870511	chr1:46148138-46245423	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
11	nsv871233	chr1:46153203-46311275	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
12	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46154600-46163000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:46154600-46169400	Weak transcription	Ovary	ovary
3	chr1:46154600-46177200	Weak transcription	Aorta	Aorta
4	chr1:46154600-46180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:46154600-46188600	Weak transcription	Fetal Heart	heart
6	chr1:46154600-46206600	Weak transcription	Brain Substantia Nigra	brain
7	chr1:46154800-46186000	Weak transcription	Psoas Muscle	Psoas
8	chr1:46154800-46192600	Weak transcription	Pancreas	Pancrea
9	chr1:46155000-46185200	Weak transcription	Colonic Mucosa	Colon
10	chr1:46155000-46187000	Weak transcription	NHLF	lung
11	chr1:46155000-46215800	Weak transcription	Small Intestine	intestine
12	chr1:46155200-46177600	Weak transcription	Fetal Brain Male	brain
13	chr1:46155200-46178800	Weak transcription	Stomach Mucosa	stomach
14	chr1:46155400-46163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:46155400-46163600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:46155600-46163600	Strong transcription	Placenta	Placenta
17	chr1:46155600-46204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:46155800-46163600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:46155800-46163600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:46155800-46163600	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:46155800-46188400	Weak transcription	Hela-S3	cervix
22	chr1:46155800-46215600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:46156000-46163000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:46156000-46163000	Strong transcription	Fetal Brain Female	brain
25	chr1:46156000-46163000	Strong transcription	Dnd41	blood
26	chr1:46156000-46163200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:46156000-46177200	Weak transcription	Lung	lung
28	chr1:46156200-46163000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:46156200-46170600	Weak transcription	HepG2	liver
30	chr1:46156400-46162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:46156400-46163000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:46156400-46163200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr1:46156600-46162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:46156600-46162800	Strong transcription	Primary T cells from cord blood	blood
35	chr1:46156600-46163000	Strong transcription	HSMM	muscle
36	chr1:46156600-46163200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:46156600-46163400	Strong transcription	Adipose Nuclei	Adipose
38	chr1:46156600-46163400	Strong transcription	Fetal Thymus	thymus
39	chr1:46156600-46163600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:46156600-46165400	Strong transcription	Fetal Intestine Large	intestine
41	chr1:46156600-46165800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:46156600-46165800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:46156800-46203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:46157000-46162800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:46157000-46164600	Weak transcription	Primary B cells from cord blood	blood
46	chr1:46157000-46166000	Strong transcription	Liver	Liver
47	chr1:46157200-46165600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:46157400-46173600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:46157400-46209800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:46157600-46163600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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