Variant report

Variant	rs11587982
Chromosome Location	chr1:46161868-46161869
allele	A/T
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:

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

Extended variants
information (count: 63 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1053941	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10749859	1.00[CHB][hapmap]
rs10789477	1.00[CHB][hapmap]
rs10890356	1.00[CHB][hapmap]
rs11211206	1.00[CHB][hapmap]
rs11211211	1.00[CHB][hapmap]
rs11211214	1.00[CHB][hapmap]
rs11579176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11582058	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs11585275	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11587918	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590549	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs12045409	1.00[CHB][hapmap]
rs28412451	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28433203	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484896	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584711	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014232	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41310432	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4364819	1.00[CHB][hapmap]
rs4423055	1.00[CHB][hapmap]
rs4434876	1.00[CHB][hapmap]
rs4557909	1.00[CHB][hapmap]
rs4660891	1.00[CHB][hapmap]
rs4660893	1.00[CHB][hapmap]
rs534534	1.00[CHB][hapmap]
rs55659201	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55951835	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56020747	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56093189	0.92[EUR][1000 genomes]
rs56238114	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56251392	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58692133	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61056720	0.80[EUR][1000 genomes]
rs6429573	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6429579	1.00[CHB][hapmap]
rs6659064	1.00[CHB][hapmap]
rs6662572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662999	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6671239	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6673894	1.00[CHB][hapmap]
rs6674105	1.00[CHB][hapmap]
rs6702764	1.00[CHB][hapmap]
rs72688452	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72688460	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7517111	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7525281	1.00[CHB][hapmap]
rs7541935	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556472	1.00[CHB][hapmap]
rs9429173	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11587982	CCDC163P	cis	Stomach	GTEx
rs11587982	CCDC163P	cis	Thyroid	GTEx
rs11587982	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs11587982	CCDC163P	cis	Whole Blood	GTEx
rs11587982	CCDC163P	cis	Heart Left Ventricle	GTEx
rs11587982	TMEM69	Cis_1M	lymphoblastoid	RTeQTL
rs11587982	CCDC163P	cis	Esophagus Muscularis	GTEx
rs11587982	CCDC163P	cis	Muscle Skeletal	GTEx
rs11587982	CCDC163P	cis	Artery Aorta	GTEx
rs11587982	CCDC163P	cis	Esophagus Mucosa	GTEx
rs11587982	CCDC163P	cis	Nerve Tibial	GTEx
rs11587982	CCDC163P	cis	lung	GTEx
rs11587982	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs11587982	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs11587982	CCDC163P	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 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	chr1:46155600-46162200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:46155600-46163600	Strong transcription	Placenta	Placenta
18	chr1:46155600-46204600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:46155800-46163600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:46155800-46163600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:46155800-46163600	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:46155800-46188400	Weak transcription	Hela-S3	cervix
23	chr1:46155800-46215600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:46156000-46162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:46156000-46163000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:46156000-46163000	Strong transcription	Fetal Brain Female	brain
27	chr1:46156000-46163000	Strong transcription	Dnd41	blood
28	chr1:46156000-46163200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:46156000-46177200	Weak transcription	Lung	lung
30	chr1:46156200-46163000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:46156200-46170600	Weak transcription	HepG2	liver
32	chr1:46156400-46162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:46156400-46163000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:46156400-46163200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:46156600-46162000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:46156600-46162400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr1:46156600-46162600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:46156600-46162800	Strong transcription	Primary T cells from cord blood	blood
39	chr1:46156600-46163000	Strong transcription	HSMM	muscle
40	chr1:46156600-46163200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:46156600-46163400	Strong transcription	Adipose Nuclei	Adipose
42	chr1:46156600-46163400	Strong transcription	Fetal Thymus	thymus
43	chr1:46156600-46163600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:46156600-46165400	Strong transcription	Fetal Intestine Large	intestine
45	chr1:46156600-46165800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:46156600-46165800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:46156800-46203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:46157000-46162800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:46157000-46164600	Weak transcription	Primary B cells from cord blood	blood
50	chr1:46157000-46166000	Strong transcription	Liver	Liver

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