Variant report

Variant	rs6666415
Chromosome Location	chr1:212582876-212582877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212581574..212584496-chr1:212586803..212589409,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065600	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11803766	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239580	0.93[AFR][1000 genomes]
rs12739715	0.99[EUR][1000 genomes]
rs12755383	1.00[EUR][1000 genomes]
rs17018997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2166155	0.95[AFR][1000 genomes]
rs35702733	0.99[EUR][1000 genomes]
rs35822123	0.83[EUR][1000 genomes]
rs4336916	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4540733	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4548507	0.86[AFR][1000 genomes]
rs6669027	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6676208	0.94[EUR][1000 genomes]
rs6693849	0.82[EUR][1000 genomes]
rs6697910	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704234	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71646158	0.83[EUR][1000 genomes]
rs71646159	0.94[EUR][1000 genomes]
rs71646161	1.00[EUR][1000 genomes]
rs7533689	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551910	1.00[EUR][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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
7	esv1828436	chr1:212577765-212591863	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv3415613	chr1:212581229-212584627	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6666415	RP11-15I11.3	cis	lung	GTEx
rs6666415	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs6666415	RP11-15I11.3	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
2	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
3	chr1:212571000-212586200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:212572600-212585000	Strong transcription	Dnd41	blood
5	chr1:212572800-212585600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:212575200-212583600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:212575200-212584400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:212575200-212585800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:212575400-212584600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:212575400-212585000	Strong transcription	Thymus	Thymus
11	chr1:212575600-212585200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:212576000-212584200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:212576000-212585200	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr1:212576200-212585200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:212576200-212585200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:212576600-212584000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:212576600-212585000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:212577000-212584200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:212577000-212584600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:212577200-212586200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:212577200-212586200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:212577600-212585000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:212577600-212585000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:212577600-212585000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:212577600-212585000	Strong transcription	NHEK	skin
26	chr1:212577800-212584000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:212577800-212584800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:212577800-212585000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:212577800-212585000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:212577800-212585000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr1:212577800-212586600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:212578000-212585000	Strong transcription	GM12878-XiMat	blood
33	chr1:212578000-212585800	Strong transcription	Primary T cells from cord blood	blood
34	chr1:212578000-212586000	Strong transcription	Fetal Thymus	thymus
35	chr1:212578400-212584600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212578400-212584600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:212578400-212584800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:212578400-212585000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:212578400-212585000	Strong transcription	K562	blood
40	chr1:212578600-212583200	Strong transcription	HMEC	breast
41	chr1:212578600-212583800	Strong transcription	A549	lung
42	chr1:212578600-212584400	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr1:212578600-212584600	Strong transcription	Primary B cells from cord blood	blood
44	chr1:212578600-212585000	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr1:212578600-212585200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:212578600-212585200	Strong transcription	Fetal Brain Female	brain
47	chr1:212578800-212584800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr1:212578800-212585000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:212579600-212585000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr1:212579800-212584200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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