Variant report

Variant	rs9846088
Chromosome Location	chr3:119183341-119183342
allele	C/G
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	MTA3	chr3:119181718-119183385	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:119181771-119183410	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:119181703-119183343	PBDE	blood:	n/a	n/a
4	POLR2A	chr3:119181952-119183346	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:119182187-119183364	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:119182116-119183540	ECC-1	luminal epithelium:	n/a	n/a
7	RUNX3	chr3:119181828-119183358	GM12878	blood:	n/a	chr3:119182048-119182057
8	JUND	chr3:119181873-119183630	SK-N-SH	brain:	n/a	chr3:119182486-119182495
9	POLR2A	chr3:119181906-119183714	HepG2	liver:	n/a	n/a
10	CREB1	chr3:119182008-119183344	GM12878	blood:	n/a	chr3:119182484-119182497
11	POLR2A	chr3:119182238-119183342	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119182024..119184224-chr3:119215586..119219856,7	MCF-7	breast:
2	chr3:119181455..119183728-chr3:119216896..119218706,2	MCF-7	breast:
3	chr3:119180899..119185941-chr3:119186195..119190279,17	K562	blood:
4	chr3:119181428..119184178-chr3:119215849..119218868,6	K562	blood:
5	chr3:119181870..119185760-chr3:119214240..119218868,7	K562	blood:
6	chr3:119181316..119183992-chr3:119395288..119397711,2	MCF-7	breast:

Variant related genes	Relation type
POGLUT1	TF binding region
TMEM39A	TF binding region
ENSG00000138495	Chromatin interaction
ENSG00000272662	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction
ENSG00000113845	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11712863	0.81[EUR][1000 genomes]
rs11713200	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2049756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3195852	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35078244	0.88[EUR][1000 genomes]
rs3772136	0.95[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3932422	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688003	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6438532	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6763561	0.89[EUR][1000 genomes]
rs6797866	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430156	0.82[LWK][hapmap];0.82[MKK][hapmap]
rs7613562	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9713715	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855347	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9872589	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9846088	POGLUT1	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119181200-119183400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:119181200-119183400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:119182000-119183400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr3:119182600-119183400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr3:119182600-119183400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:119182600-119183400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:119182600-119183400	Flanking Active TSS	Dnd41	blood
8	chr3:119182800-119183400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:119182800-119183400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr3:119182800-119183400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr3:119182800-119183400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:119183000-119183400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:119183000-119183400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr3:119183000-119183400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:119183000-119183400	Flanking Active TSS	HepG2	liver
16	chr3:119183000-119183600	Flanking Active TSS	GM12878-XiMat	blood
17	chr3:119183000-119187000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:119183000-119187200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:119183000-119187200	Weak transcription	Right Atrium	heart
20	chr3:119183000-119187400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:119183000-119187400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:119183000-119187400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:119183000-119187400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:119183000-119187400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:119183000-119187400	Weak transcription	Gastric	stomach
26	chr3:119183000-119187400	Weak transcription	Ovary	ovary
27	chr3:119183000-119187400	Weak transcription	Small Intestine	intestine
28	chr3:119183200-119183400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:119183200-119183400	Enhancers	Primary T cells from cord blood	blood
30	chr3:119183200-119183400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:119183200-119183400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:119183200-119183400	Enhancers	Brain Angular Gyrus	brain
33	chr3:119183200-119183400	Enhancers	Brain Cingulate Gyrus	brain
34	chr3:119183200-119183400	Active TSS	Brain Hippocampus Middle	brain
35	chr3:119183200-119183400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr3:119183200-119183400	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:119183200-119183400	Active TSS	A549	lung
38	chr3:119183200-119183600	Enhancers	Primary hematopoietic stem cells	blood
39	chr3:119183200-119183600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr3:119183200-119183600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr3:119183200-119183600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:119183200-119183600	Enhancers	Duodenum Mucosa	Duodenum
43	chr3:119183200-119184000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:119183200-119186800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:119183200-119186800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:119183200-119186800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:119183200-119186800	Weak transcription	Brain Substantia Nigra	brain
48	chr3:119183200-119186800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:119183200-119186800	Weak transcription	Fetal Brain Male	brain
50	chr3:119183200-119186800	Weak transcription	Right Ventricle	heart

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