Variant report

Variant	rs66478504
Chromosome Location	chr6:15387734-15387735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15386443..15388459-chr6:15400267..15402324,2	MCF-7	breast:
2	chr6:15378624..15384644-chr6:15384689..15387837,9	K562	blood:
3	chr6:15211921..15214474-chr6:15385655..15388402,2	K562	blood:
4	chr6:15247241..15250033-chr6:15387140..15388996,2	MCF-7	breast:
5	chr6:15243112..15246296-chr6:15385107..15388401,3	K562	blood:
6	chr6:15384704..15386815-chr6:15387580..15390520,2	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction
ENSG00000271888	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10484355	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10949294	0.83[ASN][1000 genomes]
rs10949295	0.83[ASN][1000 genomes]
rs11756544	0.95[ASN][1000 genomes]
rs11757415	0.95[ASN][1000 genomes]
rs12211278	0.83[ASN][1000 genomes]
rs13192347	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194410	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13195950	0.95[ASN][1000 genomes]
rs13205396	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13205612	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13208486	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214720	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16876278	0.83[ASN][1000 genomes]
rs16876354	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17576233	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17576436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17576710	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17637773	0.83[ASN][1000 genomes]
rs17638192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17638720	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237146	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299051	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299057	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34002211	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34764533	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35047303	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35139070	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364784	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35629999	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35734069	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35918625	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56123857	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56265026	0.83[ASN][1000 genomes]
rs61296041	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941859	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72836327	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7747437	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7767966	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS 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	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription 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	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15364600-15390200	Weak transcription	HepG2	liver
2	chr6:15365000-15402800	Weak transcription	Dnd41	blood
3	chr6:15367400-15389400	Weak transcription	Ovary	ovary
4	chr6:15371800-15389000	Weak transcription	Adipose Nuclei	Adipose
5	chr6:15374200-15389200	Weak transcription	HSMM	muscle
6	chr6:15376000-15389000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:15376800-15390000	Weak transcription	Aorta	Aorta
8	chr6:15377000-15389000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:15377200-15387800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:15378600-15388200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr6:15378600-15390400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr6:15379400-15390000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr6:15380400-15388400	Enhancers	Primary B cells from peripheral blood	blood
14	chr6:15380800-15389800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:15381600-15388200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr6:15381600-15390400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:15382000-15388400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr6:15382400-15388400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:15382600-15393400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:15383800-15387800	Enhancers	Brain Germinal Matrix	brain
21	chr6:15384000-15389800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:15384200-15388000	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:15384200-15390000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:15384400-15387800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:15384400-15387800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:15384400-15387800	Enhancers	Left Ventricle	heart
27	chr6:15384400-15387800	Enhancers	Psoas Muscle	Psoas
28	chr6:15384400-15390800	Enhancers	Fetal Thymus	thymus
29	chr6:15384600-15388000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:15384600-15388000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr6:15384600-15388200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:15384600-15388200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:15384600-15388400	Enhancers	Fetal Lung	lung
34	chr6:15384800-15388200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:15384800-15389000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:15384800-15389200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr6:15384800-15390800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:15385000-15387800	Enhancers	Fetal Heart	heart
39	chr6:15385000-15388000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr6:15385000-15388400	Enhancers	K562	blood
41	chr6:15385000-15390800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr6:15385000-15391800	Enhancers	Primary T cells from cord blood	blood
43	chr6:15385200-15387800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr6:15385200-15389000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr6:15385200-15389000	Weak transcription	Fetal Intestine Large	intestine
46	chr6:15385200-15389000	Weak transcription	Fetal Stomach	stomach
47	chr6:15385200-15398400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:15385400-15389000	Weak transcription	Fetal Muscle Leg	muscle
49	chr6:15385400-15389000	Weak transcription	Pancreas	Pancrea
50	chr6:15385400-15393000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links