Variant report

Variant	rs2412570
Chromosome Location	chr15:41140168-41140169
allele	C/T
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:12)
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	ZNF263	chr15:41139377-41140431	HEK293-T-REx	kidney:	n/a	chr15:41140116-41140125

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41138287..41141935-chr15:41144190..41148215,5	MCF-7	breast:
2	chr15:41131773..41133919-chr15:41138481..41140259,2	MCF-7	breast:
3	chr15:41139200..41141682-chr15:41165309..41167444,2	K562	blood:
4	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
5	chr15:41137274..41141358-chr15:41148658..41151865,7	MCF-7	breast:
6	chr15:41137927..41140333-chr15:41154449..41156600,3	MCF-7	breast:
7	chr15:41097897..41099708-chr15:41139548..41142129,2	MCF-7	breast:
8	chr15:41134891..41137417-chr15:41138433..41142150,4	MCF-7	breast:
9	chr15:41140134..41142819-chr15:41186104..41187887,2	K562	blood:
10	chr15:41134440..41137372-chr15:41139724..41141861,2	MCF-7	breast:
11	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
12	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261183	TF binding region
ENSG00000166140	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11639292	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2412569	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917953	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs622538	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs668708	0.87[EUR][1000 genomes]
rs668750	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680493	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs689589	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689594	0.90[EUR][1000 genomes]
rs689618	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689733	0.86[EUR][1000 genomes]
rs689736	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690435	0.89[EUR][1000 genomes]
rs690572	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690660	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2412570	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2412570	C15orf57	cis	Artery Tibial	GTEx
rs2412570	RP11-111A22.1	cis	Artery Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41135600-41140200	Active TSS	Rectal Smooth Muscle	rectum
2	chr15:41135600-41140400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr15:41136800-41140400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr15:41137000-41140800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
5	chr15:41137200-41140200	Enhancers	Spleen	Spleen
6	chr15:41137400-41140200	Enhancers	Primary B cells from peripheral blood	blood
7	chr15:41137400-41152200	Weak transcription	Small Intestine	intestine
8	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
9	chr15:41137600-41140200	Enhancers	Primary B cells from cord blood	blood
10	chr15:41137800-41140200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:41137800-41140200	Transcr. at gene 5' and 3'	NHEK	skin
12	chr15:41137800-41140400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr15:41137800-41140600	Enhancers	Primary hematopoietic stem cells	blood
14	chr15:41138000-41140400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:41138000-41140800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:41138000-41140800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:41138400-41140200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr15:41138400-41140200	Flanking Active TSS	Placenta	Placenta
19	chr15:41138600-41140200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr15:41138600-41140200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:41138600-41140400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:41138800-41140400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:41138800-41140600	Enhancers	Fetal Thymus	thymus
24	chr15:41138800-41140600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr15:41139000-41140200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
26	chr15:41139000-41140200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr15:41139000-41140200	Enhancers	A549	lung
28	chr15:41139000-41140400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr15:41139200-41140200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:41139200-41140200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:41139200-41140200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:41139200-41140400	Flanking Active TSS	K562	blood
33	chr15:41139400-41140200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr15:41139400-41140200	Enhancers	Fetal Lung	lung
35	chr15:41139400-41140400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:41139400-41140400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:41139400-41140800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:41139600-41140200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr15:41139600-41140200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr15:41139600-41142400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:41139800-41140200	Genic enhancers	H1 Cell Line	embryonic stem cell
42	chr15:41139800-41140200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:41139800-41140200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr15:41139800-41140400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:41139800-41140600	Active TSS	Esophagus	oesophagus
46	chr15:41139800-41140600	Enhancers	Fetal Kidney	kidney
47	chr15:41140000-41140200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr15:41140000-41140200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:41140000-41140200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr15:41140000-41140200	Enhancers	Gastric	stomach

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