Variant report

Variant	rs7849513
Chromosome Location	chr9:116077811-116077812
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116076424..116079127-chr9:116102528..116104331,2	MCF-7	breast:
2	chr9:116071625..116073462-chr9:116076376..116079141,2	K562	blood:
3	chr9:116076058..116079132-chr9:116081074..116084162,3	K562	blood:
4	chr9:116077143..116079692-chr9:116110149..116111989,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR31-1	chr9:116076583-116077893	ENSG00000248151
2	lnc-WDR31-1	chr9:116076583-116077893	NONHSAT134340

No data

Variant related genes	Relation type
ENSG00000119411	Chromatin interaction
ENSG00000148225	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10114327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10117906	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10118045	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10118275	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10124515	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10759638	0.90[CHB][hapmap]
rs10759640	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759641	0.94[EUR][1000 genomes]
rs10817475	0.85[CHB][hapmap]
rs10817476	0.81[CHB][hapmap]
rs10817481	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817485	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10981715	0.90[CHB][hapmap]
rs10981762	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10981763	0.86[ASN][1000 genomes]
rs11787602	0.87[ASN][1000 genomes]
rs11789755	0.90[CHB][hapmap]
rs12343629	0.90[CHB][hapmap]
rs1323466	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1998504	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2093691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2296073	0.90[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs3750532	0.90[CHB][hapmap]
rs3750533	0.90[CHB][hapmap]
rs3750534	0.90[CHB][hapmap]
rs3810921	0.81[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4979231	0.90[CHB][hapmap]
rs4979232	0.85[CHB][hapmap]
rs6478002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478003	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478004	0.87[ASN][1000 genomes]
rs6478005	0.87[ASN][1000 genomes]
rs6478006	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7025188	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7025371	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025517	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7025770	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7026076	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7027833	0.88[AFR][1000 genomes]
rs7041572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048039	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7850002	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7850264	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860625	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs7863921	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7864788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873862	0.81[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7849513	BSPRY	cis	Heart Left Ventricle	GTEx
rs7849513	CDC26	cis	Esophagus Muscularis	GTEx
rs7849513	CDC26	cis	Muscle Skeletal	GTEx
rs7849513	PRPF4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
3	chr9:116065400-116086800	Weak transcription	Gastric	stomach
4	chr9:116065600-116079000	Weak transcription	Fetal Intestine Small	intestine
5	chr9:116065600-116083400	Weak transcription	Esophagus	oesophagus
6	chr9:116070000-116080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:116070800-116083800	Weak transcription	Spleen	Spleen
8	chr9:116072000-116085200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:116072800-116079200	Weak transcription	Lung	lung
10	chr9:116072800-116080200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:116073000-116080400	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:116073200-116078400	Weak transcription	Pancreas	Pancrea
13	chr9:116073200-116079600	Weak transcription	Fetal Lung	lung
14	chr9:116073200-116081000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:116073800-116080000	Weak transcription	Adipose Nuclei	Adipose
16	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:116074000-116079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:116074600-116079800	Weak transcription	Left Ventricle	heart
19	chr9:116074600-116080600	Weak transcription	Right Ventricle	heart
20	chr9:116075800-116078400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:116075800-116079000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:116076000-116084600	Weak transcription	HSMMtube	muscle
23	chr9:116076200-116078400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:116076200-116081000	Weak transcription	Fetal Muscle Leg	muscle
25	chr9:116076200-116085000	Weak transcription	Placenta	Placenta
26	chr9:116076400-116078800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:116076400-116081000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr9:116076600-116078800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:116077000-116079000	Weak transcription	Fetal Intestine Large	intestine
30	chr9:116077000-116080600	Weak transcription	Fetal Kidney	kidney
31	chr9:116077000-116086800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:116077200-116085600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:116077400-116079200	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:116077400-116080600	Weak transcription	Brain Angular Gyrus	brain
35	chr9:116077400-116080600	Weak transcription	Brain Substantia Nigra	brain
36	chr9:116077400-116082800	Weak transcription	Colonic Mucosa	Colon
37	chr9:116077400-116083800	Strong transcription	Ovary	ovary
38	chr9:116077400-116084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:116077400-116084200	Strong transcription	Fetal Stomach	stomach
40	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
41	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:116077600-116079400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:116077600-116079600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr9:116077600-116080400	Weak transcription	Fetal Brain Male	brain
45	chr9:116077800-116078800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:116077800-116079000	Weak transcription	Brain Anterior Caudate	brain
47	chr9:116077800-116082400	Weak transcription	Aorta	Aorta
48	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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