Variant report

Variant	rs776696
Chromosome Location	chr15:42349347-42349348
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42273351..42275852-chr15:42348244..42350332,2	MCF-7	breast:
2	chr15:42281453..42282403-chr15:42348797..42349914,6	K562	blood:
3	chr15:42281405..42281926-chr15:42348985..42349752,2	MCF-7	breast:
4	chr15:42281382..42282364-chr15:42348961..42349921,14	MCF-7	breast:
5	chr15:42284477..42286944-chr15:42348245..42350387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188089	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1668585	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs1668589	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs1668596	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1712430	0.93[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs1712435	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs600415	0.83[CHB][hapmap]
rs605253	0.84[CHB][hapmap];0.87[EUR][1000 genomes]
rs614215	0.83[CHB][hapmap]
rs776688	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs776689	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs776691	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs776702	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs776726	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1043641	chr15:42336584-42381240	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv904131	chr15:42343794-42390223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42343000-42357600	Weak transcription	Lung	lung
2	chr15:42348800-42349400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr15:42348800-42349400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr15:42348800-42349600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr15:42348800-42349800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr15:42348800-42350200	Enhancers	Fetal Heart	heart
7	chr15:42349000-42349400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
8	chr15:42349000-42349400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:42349000-42349400	Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr15:42349000-42349400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr15:42349000-42349400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:42349000-42349400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:42349000-42349400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:42349000-42349400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:42349000-42349400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:42349000-42349400	Active TSS	Brain Anterior Caudate	brain
17	chr15:42349000-42349400	Active TSS	Brain Germinal Matrix	brain
18	chr15:42349000-42349400	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr15:42349000-42349400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr15:42349000-42349400	Active TSS	Psoas Muscle	Psoas
21	chr15:42349000-42349400	Active TSS	Rectal Smooth Muscle	rectum
22	chr15:42349000-42349400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
23	chr15:42349000-42349400	Bivalent Enhancer	Thymus	Thymus
24	chr15:42349000-42349400	Bivalent/Poised TSS	HSMMtube	muscle
25	chr15:42349000-42349400	Flanking Active TSS	NH-A	brain
26	chr15:42349000-42349600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:42349000-42349600	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:42349000-42349600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
29	chr15:42349000-42349600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
30	chr15:42349000-42349600	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr15:42349000-42349600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
32	chr15:42349000-42349600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:42349000-42349600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
34	chr15:42349000-42349600	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr15:42349000-42349600	Bivalent Enhancer	Fetal Brain Male	brain
36	chr15:42349000-42349600	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr15:42349000-42349600	Enhancers	Fetal Lung	lung
38	chr15:42349000-42349600	Flanking Active TSS	Placenta	Placenta
39	chr15:42349000-42349600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr15:42349000-42349600	Flanking Active TSS	HMEC	breast
41	chr15:42349000-42349600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr15:42349000-42349600	Flanking Active TSS	NHEK	skin
43	chr15:42349000-42349800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr15:42349000-42349800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:42349000-42349800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:42349000-42349800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:42349000-42349800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr15:42349000-42349800	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr15:42349000-42349800	Active TSS	Right Ventricle	heart
50	chr15:42349000-42349800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links