Variant report

Variant	rs9839527
Chromosome Location	chr3:160994690-160994691
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
2	chr3:160992723..160996276-chr3:161021665..161023883,3	MCF-7	breast:
3	chr3:160992583..160995712-chr3:161006155..161008165,3	MCF-7	breast:
4	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
5	chr3:160987260..160989063-chr3:160992148..160994885,3	MCF-7	breast:
6	chr3:160984342..160995741-chr3:161044454..161065477,51	MCF-7	breast:
7	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:
8	chr3:160982688..160996909-chr3:161122010..161144833,109	MCF-7	breast:
9	chr3:160990275..160995115-chr3:161003197..161013240,19	MCF-7	breast:
10	chr3:160992668..160995441-chr3:161067329..161069400,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000240567	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1026572	0.82[AMR][1000 genomes]
rs1154701	0.90[EUR][1000 genomes]
rs12486253	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495310	0.99[EUR][1000 genomes]
rs13083229	0.99[EUR][1000 genomes]
rs1478568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1904204	0.80[ASN][1000 genomes]
rs336572	0.81[AMR][1000 genomes]
rs3849524	0.81[EUR][1000 genomes]
rs4290817	0.97[EUR][1000 genomes]
rs4470535	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4518145	0.86[EUR][1000 genomes]
rs4560315	0.99[EUR][1000 genomes]
rs4856714	0.98[EUR][1000 genomes]
rs4856738	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4856739	0.89[EUR][1000 genomes]
rs4856767	1.00[EUR][1000 genomes]
rs4856768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55688744	0.95[EUR][1000 genomes]
rs6441370	0.90[EUR][1000 genomes]
rs6441371	0.88[EUR][1000 genomes]
rs6768818	0.97[EUR][1000 genomes]
rs6774276	0.85[EUR][1000 genomes]
rs6789388	0.89[EUR][1000 genomes]
rs6791213	0.95[EUR][1000 genomes]
rs6809256	0.96[EUR][1000 genomes]
rs7611367	0.90[EUR][1000 genomes]
rs7613227	0.95[EUR][1000 genomes]
rs7613358	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7627528	0.99[EUR][1000 genomes]
rs7632797	0.90[EUR][1000 genomes]
rs7633186	0.89[EUR][1000 genomes]
rs7636941	0.98[EUR][1000 genomes]
rs7647327	0.81[EUR][1000 genomes]
rs7652267	0.98[EUR][1000 genomes]
rs7653233	0.81[EUR][1000 genomes]
rs7653361	0.81[EUR][1000 genomes]
rs899275	0.95[EUR][1000 genomes]
rs9290069	0.82[AMR][1000 genomes]
rs9790314	0.81[EUR][1000 genomes]
rs9809522	0.99[EUR][1000 genomes]
rs9815222	1.00[EUR][1000 genomes]
rs9821201	0.81[EUR][1000 genomes]
rs9834659	0.99[EUR][1000 genomes]
rs9850455	0.81[EUR][1000 genomes]
rs9864752	0.88[EUR][1000 genomes]
rs9870059	0.81[EUR][1000 genomes]

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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9839527	SPTSSB	cis	Heart Left Ventricle	GTEx
rs9839527	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:160975400-160995800	Weak transcription	Fetal Intestine Large	intestine
11	chr3:160976600-160995400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:160979200-160999800	Weak transcription	Psoas Muscle	Psoas
13	chr3:160982200-160995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:160982200-160995400	Weak transcription	Aorta	Aorta
15	chr3:160982400-160996600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:160984800-160995200	Weak transcription	A549	lung
17	chr3:160984800-161002400	Weak transcription	NHEK	skin
18	chr3:160985200-160996600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:160988000-160996200	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:160989000-161000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:160991800-160996000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:160992200-160995200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:160993200-160994800	Strong transcription	HSMM	muscle
24	chr3:160994200-160995400	Weak transcription	Colonic Mucosa	Colon
25	chr3:160994200-160995400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:160994200-160995600	Weak transcription	Fetal Brain Male	brain
27	chr3:160994200-160995800	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr3:160994200-160995800	Weak transcription	Gastric	stomach
29	chr3:160994400-160995000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:160994400-160995200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:160994400-160995400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:160994400-160995400	Weak transcription	Liver	Liver
33	chr3:160994400-160995400	Weak transcription	Pancreas	Pancrea
34	chr3:160994400-160996800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:160994400-160997600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:160994400-160997600	Weak transcription	Left Ventricle	heart
37	chr3:160994600-160995600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:160994600-161002200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart

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