Variant report

Variant	rs13076269
Chromosome Location	chr3:48675925-48675926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48675905-48676590	K562	blood:	n/a	n/a
2	POLR2A	chr3:48675824-48676272	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48675163..48677992-chr3:48697938..48699928,2	K562	blood:
2	chr3:48671609..48675358-chr3:48675367..48678236,4	K562	blood:
3	chr3:48670750..48673706-chr3:48674188..48676105,2	MCF-7	breast:
4	chr3:48592512..48594363-chr3:48675135..48677320,2	K562	blood:
5	chr3:48645479..48647283-chr3:48674459..48676978,2	MCF-7	breast:
6	chr3:48675462..48677600-chr3:48699390..48701510,3	MCF-7	breast:
7	chr3:48673914..48675991-chr3:48685883..48687496,2	K562	blood:
8	chr3:48675163..48676738-chr3:48698428..48701202,2	K562	blood:

No data

Variant related genes	Relation type
SLC26A6	TF binding region
ENSG00000010256	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11557629	0.81[AMR][1000 genomes]
rs11706203	0.81[AMR][1000 genomes]
rs11706983	0.81[AMR][1000 genomes]
rs11719291	0.81[AMR][1000 genomes]
rs12107252	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12107418	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12715429	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13063312	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13070798	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090013	0.81[AMR][1000 genomes]
rs13096357	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316551	0.81[AMR][1000 genomes]
rs13324119	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324142	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13434258	0.81[AMR][1000 genomes]
rs17080319	0.81[AMR][1000 genomes]
rs2276850	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276852	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286651	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286652	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2302295	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2310996	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2310997	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28452701	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28567949	0.81[AMR][1000 genomes]
rs28657585	0.81[AMR][1000 genomes]
rs34096717	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34153629	0.81[AMR][1000 genomes]
rs34368826	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34577723	0.83[AMR][1000 genomes]
rs34638686	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35064573	0.81[AMR][1000 genomes]
rs35343040	0.81[ASN][1000 genomes]
rs3733086	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3806694	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821875	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821876	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57334642	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6768448	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6773261	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792156	0.83[ASN][1000 genomes]
rs68042649	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs740787	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7620853	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631574	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809222	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9811027	0.81[AMR][1000 genomes]
rs9811318	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9812200	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9821797	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9830581	0.81[ASN][1000 genomes]
rs9836462	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9841602	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9843316	0.81[ASN][1000 genomes]
rs9868809	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9873726	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9878063	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription 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 miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13076269	WDR6	cis	Esophagus Mucosa	GTEx
rs13076269	WDR6	cis	Adipose Subcutaneous	GTEx
rs13076269	SLC26A6	cis	lung	GTEx
rs13076269	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs13076269	SLC26A6	cis	Muscle Skeletal	GTEx
rs13076269	WDR6	cis	lung	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48673600-48693400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:48673800-48676400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:48673800-48676800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:48673800-48678000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:48673800-48678400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:48673800-48692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:48674000-48676600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:48674000-48676600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:48674000-48676600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:48674000-48676800	Weak transcription	NHEK	skin
11	chr3:48674000-48677200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:48674000-48678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:48674000-48681400	Weak transcription	Pancreas	Pancrea
14	chr3:48674000-48683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:48674000-48692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:48674000-48693400	Weak transcription	Fetal Brain Male	brain
17	chr3:48674000-48693600	Weak transcription	Brain Substantia Nigra	brain
18	chr3:48674200-48676600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:48674200-48676800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:48674200-48676800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:48674200-48692600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:48674400-48676400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:48674400-48676600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:48674400-48677200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:48674400-48677800	Weak transcription	Dnd41	blood
26	chr3:48674400-48682000	Weak transcription	Right Atrium	heart
27	chr3:48674400-48685800	Weak transcription	Fetal Intestine Large	intestine
28	chr3:48674400-48691000	Weak transcription	Spleen	Spleen
29	chr3:48674400-48692800	Weak transcription	Placenta	Placenta
30	chr3:48674400-48692800	Weak transcription	Right Ventricle	heart
31	chr3:48674400-48693600	Weak transcription	Gastric	stomach
32	chr3:48674600-48676400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:48674600-48678600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:48674800-48676600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:48674800-48676600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:48674800-48676600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:48674800-48676800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:48674800-48677000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:48674800-48678400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:48674800-48692600	Strong transcription	Fetal Brain Female	brain
41	chr3:48674800-48695600	Weak transcription	Hela-S3	cervix
42	chr3:48675000-48676000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:48675000-48676400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:48675000-48676600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:48675000-48676800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:48675000-48677600	Genic enhancers	Brain Germinal Matrix	brain
47	chr3:48675000-48689200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:48675000-48693600	Weak transcription	A549	lung
49	chr3:48675000-48694200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:48675000-48697200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links