Variant report

Variant	rs9868809
Chromosome Location	chr3:48681053-48681054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr3:48680992-48681086	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48670869..48673258-chr3:48680752..48682540,2	K562	blood:
2	chr3:48680179..48682493-chr3:48699784..48702712,4	MCF-7	breast:

Variant related genes	Relation type
CELSR3	TF binding region
ENSG00000225697	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11706983	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs12107252	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs12107418	0.81[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs12715429	0.85[EUR][1000 genomes]
rs13063312	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13070798	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs13076269	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13096357	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13324119	0.85[EUR][1000 genomes]
rs13324142	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13434258	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs17080289	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs2276850	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276852	0.90[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2286651	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2286652	1.00[ASW][hapmap];0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2302295	0.90[EUR][1000 genomes]
rs2310996	0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2310997	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452701	0.85[EUR][1000 genomes]
rs34096717	0.85[EUR][1000 genomes]
rs34368826	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34638686	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs3733086	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3806694	0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821875	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3821876	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3895736	0.82[MKK][hapmap]
rs57334642	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6768448	0.81[EUR][1000 genomes]
rs6773261	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792156	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs68042649	0.81[EUR][1000 genomes]
rs73078349	0.81[EUR][1000 genomes]
rs740787	0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7620853	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7631574	0.90[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9809222	0.81[EUR][1000 genomes]
rs9811318	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs9812200	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs9821797	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9830581	0.84[ASW][hapmap];0.83[GIH][hapmap]
rs9836462	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs9841602	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs9843316	0.80[CHD][hapmap];0.83[GIH][hapmap]
rs9871180	0.83[GIH][hapmap]
rs9873726	0.81[EUR][1000 genomes]
rs9878063	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9881877	0.83[GIH][hapmap]
rs9882549	0.83[GIH][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9868809	WDR6	cis	Adipose Subcutaneous	GTEx
rs9868809	WDR6	cis	lymphoblastoid	seeQTL
rs9868809	WDR6	cis	Esophagus Mucosa	GTEx
rs9868809	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9868809	SLC26A6	cis	lung	GTEx

Chromatin state (count:56 , 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	chr3:48673800-48692800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:48674000-48681400	Weak transcription	Pancreas	Pancrea
4	chr3:48674000-48683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:48674000-48692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr3:48674000-48693400	Weak transcription	Fetal Brain Male	brain
7	chr3:48674000-48693600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:48674200-48692600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:48674400-48682000	Weak transcription	Right Atrium	heart
10	chr3:48674400-48685800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:48674400-48691000	Weak transcription	Spleen	Spleen
12	chr3:48674400-48692800	Weak transcription	Placenta	Placenta
13	chr3:48674400-48692800	Weak transcription	Right Ventricle	heart
14	chr3:48674400-48693600	Weak transcription	Gastric	stomach
15	chr3:48674800-48692600	Strong transcription	Fetal Brain Female	brain
16	chr3:48674800-48695600	Weak transcription	Hela-S3	cervix
17	chr3:48675000-48689200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:48675000-48693600	Weak transcription	A549	lung
19	chr3:48675000-48694200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:48675000-48697200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:48675200-48687400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:48675200-48692400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48675400-48686200	Weak transcription	HepG2	liver
24	chr3:48676400-48684600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr3:48676400-48687400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:48676400-48689200	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:48676600-48681400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:48676600-48684400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:48676600-48684400	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr3:48676600-48687200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr3:48676600-48687200	Strong transcription	Brain Angular Gyrus	brain
32	chr3:48676600-48691800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:48676800-48684600	Strong transcription	Brain Anterior Caudate	brain
34	chr3:48676800-48684600	Strong transcription	Brain Cingulate Gyrus	brain
35	chr3:48677000-48687200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:48677400-48686000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:48677600-48692200	Strong transcription	Brain Germinal Matrix	brain
38	chr3:48678400-48682800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:48678400-48683800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:48678400-48684400	Strong transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:48678600-48684000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:48678800-48684600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:48679600-48681600	Strong transcription	Fetal Intestine Small	intestine
44	chr3:48679600-48684400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:48679800-48681200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:48680000-48695400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:48680200-48684000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:48680400-48682200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:48680600-48682200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:48680800-48681200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links