Variant report

Variant	rs8039284
Chromosome Location	chr15:75492459-75492460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75492412-75497603	GM18505	blood:	n/a	n/a
2	POLR2A	chr15:75490327-75497524	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:75492219-75497525	GM12878	blood:	n/a	n/a
4	MTA3	chr15:75490439-75497753	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:75490585-75499135	GM12878	blood:	n/a	n/a
6	RFX5	chr15:75492387-75492501	Hela-S3	cervix:	n/a	chr15:75492428-75492443
7	POLR2A	chr15:75490225-75497776	GM12878	blood:	n/a	n/a
8	RFX5	chr15:75492335-75492518	HepG2	liver:	n/a	chr15:75492428-75492443
9	POLR2A	chr15:75489631-75513671	GM12878	blood:	n/a	n/a
10	GATA1	chr15:75492053-75492581	PBDE	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
2	chr15:75470196..75472288-chr15:75492167..75494098,2	K562	blood:
3	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
4	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
5	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
6	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
7	chr15:75405088..75407275-chr15:75491436..75494556,3	MCF-7	breast:
8	chr15:75487202..75491376-chr15:75491587..75495203,5	K562	blood:
9	chr15:75486189..75488237-chr15:75491823..75494086,2	MCF-7	breast:
10	chr15:75490684..75493339-chr15:75497415..75499804,2	K562	blood:
11	chr15:75492389..75494597-chr8:145752169..145754298,2	MCF-7	breast:
12	chr15:75488848..75492298-chr15:75492406..75495739,4	MCF-7	breast:
13	chr15:75477700..75479387-chr15:75492353..75494507,2	MCF-7	breast:
14	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:

No data

Variant related genes	Relation type
C15orf39	TF binding region
ENSG00000260152	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000240366	Chromatin interaction
ENSG00000254402	Chromatin interaction
ENSG00000213563	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10851879	0.81[AFR][1000 genomes]
rs11072532	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11072533	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11072534	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11072536	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11636245	0.85[CHB][hapmap]
rs11853027	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12591506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12592411	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12708517	0.89[ASN][1000 genomes]
rs12904018	0.90[ASN][1000 genomes]
rs1466663	0.81[AFR][1000 genomes]
rs1532155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1976191	0.90[AFR][1000 genomes]
rs2006683	0.84[ASN][1000 genomes]
rs3743210	0.93[ASN][1000 genomes]
rs3743211	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4886428	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4886430	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886431	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4886677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7182402	0.81[AFR][1000 genomes]
rs7403344	0.92[ASN][1000 genomes]
rs8025431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8027407	1.00[AFR][1000 genomes]
rs8043432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs902482	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs953555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv1053212	chr15:75428467-75534408	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75477200-75492600	Weak transcription	Spleen	Spleen
2	chr15:75484200-75492800	Enhancers	Placenta	Placenta
3	chr15:75487800-75493200	Weak transcription	Brain Substantia Nigra	brain
4	chr15:75488000-75493200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:75488200-75493400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:75488400-75492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:75488400-75493200	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:75488600-75493400	Weak transcription	Ovary	ovary
9	chr15:75488800-75492800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:75489800-75492600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:75489800-75493200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:75490400-75492600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:75490400-75493200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:75490600-75492600	Enhancers	Fetal Intestine Small	intestine
15	chr15:75490600-75492600	Enhancers	Stomach Mucosa	stomach
16	chr15:75490600-75493200	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:75490600-75493200	Flanking Active TSS	HepG2	liver
18	chr15:75490800-75492600	Enhancers	Fetal Intestine Large	intestine
19	chr15:75490800-75493000	Enhancers	Gastric	stomach
20	chr15:75490800-75493200	Enhancers	Thymus	Thymus
21	chr15:75490800-75493200	Enhancers	K562	blood
22	chr15:75491000-75492600	Weak transcription	Pancreas	Pancrea
23	chr15:75491000-75493400	Weak transcription	Brain Anterior Caudate	brain
24	chr15:75491200-75492600	Enhancers	H9 Cell Line	embryonic stem cell
25	chr15:75491200-75492600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr15:75491200-75492800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:75491200-75493200	Enhancers	Primary T cells from cord blood	blood
28	chr15:75491200-75493200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr15:75491200-75493600	Enhancers	Lung	lung
30	chr15:75491200-75494000	Flanking Active TSS	GM12878-XiMat	blood
31	chr15:75491200-75494000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr15:75491400-75492600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:75491400-75492600	Weak transcription	A549	lung
34	chr15:75491400-75492800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr15:75491400-75492800	Enhancers	Esophagus	oesophagus
36	chr15:75491400-75493400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:75491600-75492600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:75491600-75492800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:75491600-75492800	Enhancers	Colonic Mucosa	Colon
40	chr15:75491600-75493200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:75491600-75493200	Enhancers	Adipose Nuclei	Adipose
42	chr15:75491600-75493200	Weak transcription	Liver	Liver
43	chr15:75491600-75493200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr15:75491800-75492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:75491800-75492800	Enhancers	HMEC	breast
46	chr15:75491800-75493000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:75491800-75493200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr15:75491800-75493400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:75491800-75493400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr15:75492000-75492600	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links