Variant report

Variant	rs2470686
Chromosome Location	chr15:45341718-45341719
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:57)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:57 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT5A	chr15:45340865-45341824	K562	blood:	n/a	n/a
2	ARID3A	chr15:45340769-45342008	K562	blood:	n/a	n/a
3	GATA1	chr15:45340494-45341850	K562	blood:	n/a	n/a
4	BHLHE40	chr15:45340918-45341750	K562	blood:	n/a	n/a
5	CBX3	chr15:45340701-45341756	K562	blood:	n/a	n/a
6	ATF1	chr15:45340852-45341865	K562	blood:	n/a	n/a
7	TRIM28	chr15:45340716-45341862	K562	blood:	n/a	n/a
8	GATA2	chr15:45340749-45341849	K562	blood:	n/a	n/a
9	TEAD4	chr15:45340804-45341853	K562	blood:	n/a	n/a
10	JUND	chr15:45340829-45341883	K562	blood:	n/a	n/a
11	GATA1	chr15:45340925-45341837	PBDEFetal	blood:	n/a	n/a
12	GATA2	chr15:45340834-45341751	K562	blood:	n/a	n/a
13	SETDB1	chr15:45340696-45341730	K562	blood:	n/a	n/a
14	EP300	chr15:45340958-45341741	K562	blood:	n/a	n/a
15	ZNF384	chr15:45340917-45341768	K562	blood:	n/a	n/a
16	IRF1	chr15:45340787-45342007	K562	blood:	n/a	n/a
17	JUN	chr15:45340753-45341845	K562	blood:	n/a	n/a
18	CEBPD	chr15:45340771-45341814	K562	blood:	n/a	n/a
19	ZNF274	chr15:45340943-45341873	K562	blood:	n/a	n/a
20	RCOR1	chr15:45340900-45341862	K562	blood:	n/a	n/a
21	GATA2	chr15:45340894-45341782	K562	blood:	n/a	n/a
22	PML	chr15:45340843-45341831	K562	blood:	n/a	n/a
23	IRF1	chr15:45340810-45341834	K562	blood:	n/a	n/a
24	KAP1	chr15:45340624-45341833	K562	blood:	n/a	n/a
25	GATA1	chr15:45340587-45342035	PBDE	blood:	n/a	n/a
26	TEAD4	chr15:45340711-45341871	K562	blood:	n/a	n/a
27	MAZ	chr15:45340807-45341876	K562	blood:	n/a	n/a
28	NR2F2	chr15:45340783-45341896	K562	blood:	n/a	n/a
29	MYC	chr15:45340818-45341881	K562	blood:	n/a	n/a
30	TBL1XR1	chr15:45340918-45341763	K562	blood:	n/a	n/a
31	CUX1	chr15:45340952-45342048	K562	blood:	n/a	n/a
32	POLR2A	chr15:45340879-45341810	K562	blood:	n/a	n/a
33	POLR2A	chr15:45340918-45341884	K562	blood:	n/a	n/a
34	CBX3	chr15:45340584-45341975	K562	blood:	n/a	n/a
35	NR2F2	chr15:45340707-45341851	K562	blood:	n/a	n/a
36	CEBPB	chr15:45340905-45341776	K562	blood:	n/a	n/a
37	RCOR1	chr15:45340805-45341884	K562	blood:	n/a	n/a
38	CCNT2	chr15:45340869-45341881	K562	blood:	n/a	n/a
39	JUN	chr15:45340903-45342150	K562	blood:	n/a	n/a
40	PML	chr15:45340853-45341814	K562	blood:	n/a	n/a
41	MXI1	chr15:45341002-45341722	K562	blood:	n/a	n/a
42	EP300	chr15:45340793-45341953	K562	blood:	n/a	n/a
43	HCFC1	chr15:45340932-45341763	K562	blood:	n/a	n/a
44	STAT5A	chr15:45340790-45341857	K562	blood:	n/a	n/a
45	CREB1	chr15:45340825-45341887	K562	blood:	n/a	n/a
46	POLR2A	chr15:45340895-45341779	K562	blood:	n/a	n/a
47	ATF3	chr15:45340918-45341824	K562	blood:	n/a	n/a
48	SETDB1	chr15:45340563-45343706	K562	blood:	n/a	n/a
49	UBTF	chr15:45340951-45341743	K562	blood:	n/a	n/a
50	ZMIZ1	chr15:45340931-45341744	K562	blood:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000252171	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11070436	1.00[CEU][hapmap]
rs11070439	1.00[CEU][hapmap]
rs11634731	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635836	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs11636558	1.00[CEU][hapmap]
rs11637679	1.00[CEU][hapmap]
rs12441189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12902975	1.00[CEU][hapmap]
rs12903829	0.81[ASN][1000 genomes]
rs12913288	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs13380326	1.00[CEU][hapmap]
rs1704792	0.82[CEU][hapmap]
rs199138	0.82[CHB][hapmap]
rs2036831	1.00[CEU][hapmap];0.84[GIH][hapmap]
rs2437866	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2467841	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2467843	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470658	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2554451	0.82[CHB][hapmap]
rs269863	0.82[CHB][hapmap]
rs269868	0.82[CHB][hapmap]
rs2854446	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35628479	0.87[EUR][1000 genomes]
rs3759890	1.00[CEU][hapmap]
rs3874239	0.90[EUR][1000 genomes]
rs452762	1.00[CEU][hapmap];0.81[GIH][hapmap]
rs4775707	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58232764	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7165595	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167120	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs925350	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs963002	1.00[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	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv977710	chr15:45316191-45360995	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv3438009	chr15:45329164-45353245	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv9260	chr15:45334818-45344949	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
9	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2470686	SORD	cis	Skin Sun Exposed Lower leg	GTEx
rs2470686	CTD-2008A1.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2470686	RP11-109D20.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2470686	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45316400-45342200	Weak transcription	HSMMtube	muscle
2	chr15:45316400-45342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:45316600-45344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:45316600-45351000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:45316600-45356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:45316600-45366600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:45316800-45346400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:45319200-45363200	Weak transcription	Fetal Thymus	thymus
9	chr15:45319800-45363600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:45323800-45342600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:45327600-45344400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:45329400-45342400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:45329400-45356400	Weak transcription	Osteobl	bone
14	chr15:45329600-45350000	Weak transcription	A549	lung
15	chr15:45329800-45343600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:45329800-45343800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr15:45329800-45345600	Weak transcription	Fetal Kidney	kidney
18	chr15:45329800-45350200	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:45329800-45365800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:45331400-45369600	Weak transcription	Pancreas	Pancrea
21	chr15:45333400-45361200	Weak transcription	HUVEC	blood vessel
22	chr15:45336000-45342600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:45336800-45347400	Weak transcription	Adipose Nuclei	Adipose
24	chr15:45337400-45365400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:45338000-45343600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:45338000-45363800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr15:45338400-45365200	Weak transcription	HSMM	muscle
28	chr15:45338600-45345600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:45339000-45345800	Strong transcription	Liver	Liver
30	chr15:45339400-45342200	Strong transcription	HepG2	liver
31	chr15:45339400-45345600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:45339600-45343000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:45339800-45342800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:45339800-45345600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:45340000-45341800	ZNF genes & repeats	GM12878-XiMat	blood
36	chr15:45340000-45341800	Strong transcription	NHEK	skin
37	chr15:45340000-45342000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:45340000-45342000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr15:45340000-45342000	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr15:45340000-45343400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:45340000-45345000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:45340000-45345800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr15:45340400-45342000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr15:45340400-45345800	Strong transcription	Hela-S3	cervix
45	chr15:45340600-45341800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
46	chr15:45340600-45341800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:45340600-45341800	Enhancers	Stomach Mucosa	stomach
48	chr15:45340600-45341800	ZNF genes & repeats	Thymus	Thymus
49	chr15:45340600-45341800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr15:45340600-45342000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links