Variant report

Variant	rs6492939
Chromosome Location	chr15:40561890-40561891
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40561884-40567478	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40326501..40329204-chr15:40561797..40564190,2	K562	blood:
2	chr15:40556187..40558733-chr15:40561114..40563501,3	K562	blood:
3	chr15:40556498..40560954-chr15:40561713..40567483,5	MCF-7	breast:
4	chr15:40559456..40563517-chr15:40563540..40567846,5	K562	blood:
5	chr15:40534412..40536720-chr15:40560933..40563065,2	K562	blood:
6	chr15:40560518..40564968-chr15:40571424..40575793,5	K562	blood:
7	chr15:40560369..40562602-chr15:40585319..40587602,2	K562	blood:
8	chr15:40531413..40533988-chr15:40561455..40564026,2	MCF-7	breast:
9	chr15:40527496..40529447-chr15:40561736..40564505,3	K562	blood:

No data

Variant related genes	Relation type
PAK6	TF binding region
ENSG00000137843	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000230778	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12148261	1.00[CHB][hapmap]
rs12902461	0.81[EUR][1000 genomes]
rs1494533	1.00[CHB][hapmap]
rs17668261	1.00[CHB][hapmap]
rs17668415	1.00[CHB][hapmap]
rs1801389	1.00[CHB][hapmap]
rs3743131	0.84[YRI][hapmap]
rs3759843	1.00[CHB][hapmap]
rs6492940	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162809	0.81[EUR][1000 genomes]
rs7165187	1.00[CHB][hapmap]
rs7173181	1.00[CHB][hapmap]
rs7182070	1.00[CHB][hapmap]
rs8034871	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037267	0.87[ASW][hapmap]
rs936215	1.00[MEX][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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv904096	chr15:40550149-40604777	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv904097	chr15:40555065-40595627	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv517541	chr15:40557268-40595627	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
2	chr15:40546200-40568200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:40550000-40568000	Weak transcription	Spleen	Spleen
4	chr15:40550400-40566800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:40551400-40571000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:40553800-40570400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:40555400-40566600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:40556200-40567400	Strong transcription	Fetal Intestine Small	intestine
9	chr15:40556200-40567600	Weak transcription	Colonic Mucosa	Colon
10	chr15:40557000-40568200	Weak transcription	Lung	lung
11	chr15:40557200-40562000	Strong transcription	Fetal Intestine Large	intestine
12	chr15:40557200-40571800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:40557400-40566800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:40559000-40564600	Weak transcription	Gastric	stomach
15	chr15:40559000-40570000	Weak transcription	Brain Anterior Caudate	brain
16	chr15:40559200-40568000	Weak transcription	Brain Germinal Matrix	brain
17	chr15:40559200-40570000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:40559400-40562800	Weak transcription	Placenta	Placenta
19	chr15:40559400-40570200	Weak transcription	Brain Angular Gyrus	brain
20	chr15:40559400-40571600	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:40559600-40563000	Strong transcription	NHEK	skin
22	chr15:40559600-40564600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:40559600-40567200	Weak transcription	Stomach Mucosa	stomach
24	chr15:40559600-40568800	Weak transcription	Fetal Brain Female	brain
25	chr15:40559600-40569000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:40559600-40569200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:40559600-40570000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:40559600-40570400	Strong transcription	Esophagus	oesophagus
29	chr15:40559600-40571800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:40559800-40564000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:40559800-40567000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr15:40560200-40566600	Weak transcription	K562	blood
33	chr15:40560200-40568200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:40560400-40564600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:40560400-40566600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:40560600-40563600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr15:40560600-40567200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr15:40560600-40567200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:40560800-40571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:40561000-40563800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:40561000-40564400	Weak transcription	Pancreas	Pancrea
42	chr15:40561000-40564600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:40561200-40562600	Weak transcription	HMEC	breast
44	chr15:40561800-40562000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr15:40561800-40562000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:40561800-40562200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr15:40561800-40567200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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