Variant report

Variant	rs1169091
Chromosome Location	chr12:122462486-122462487
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr12:122458987-122462622	IMR90	lung:	n/a	n/a
2	STAT5A	chr12:122462349-122462600	GM12878	blood:	n/a	n/a
3	MTA3	chr12:122462042-122462529	GM12878	blood:	n/a	n/a
4	TCF12	chr12:122460784-122462564	A549	lung:	n/a	chr12:122461929-122461936 chr12:122461930-122461940
5	POLR2A	chr12:122460754-122462553	SK-N-SH	brain:	n/a	n/a
6	MXI1	chr12:122458857-122462827	SK-N-SH	brain:	n/a	n/a
7	TEAD4	chr12:122462152-122462631	K562	blood:	n/a	n/a
8	MYC	chr12:122462258-122462680	MCF10A-Er-Src	breast:	n/a	n/a
9	RUNX3	chr12:122462105-122462656	GM12878	blood:	n/a	n/a
10	NR2F2	chr12:122461056-122462550	K562	blood:	n/a	n/a
11	NFYB	chr12:122462260-122462637	GM12878	blood:	n/a	chr12:122462486-122462496
12	RUNX3	chr12:122461475-122462717	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:122460342-122463264	Raji	blood:	n/a	n/a
14	ZNF384	chr12:122462243-122462493	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122235921..122238772-chr12:122461316..122462876,2	K562	blood:
2	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
3	chr12:122237430..122243628-chr12:122458689..122463112,11	MCF-7	breast:
4	chr12:122356337..122361793-chr12:122458841..122462522,5	MCF-7	breast:
5	chr12:122325408..122328152-chr12:122461584..122463358,2	K562	blood:
6	chr12:122428522..122431508-chr12:122460147..122462626,2	MCF-7	breast:
7	chr12:122393562..122396353-chr12:122460972..122463920,2	K562	blood:
8	chr12:122369123..122373485-chr12:122458454..122462950,5	K562	blood:
9	chr12:122461383..122462889-chr12:122756023..122758589,2	K562	blood:
10	chr12:122460064..122462817-chr12:122499395..122500991,2	MCF-7	breast:
11	chr12:122460432..122462517-chr12:122503179..122505981,2	MCF-7	breast:
12	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
13	chr12:122459539..122463256-chr12:122498402..122502892,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255856	TF binding region
ENSG00000110801	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1168658	0.86[MEX][hapmap];0.87[TSI][hapmap]
rs1169076	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1169081	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1169083	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1169084	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1169086	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1169087	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1169089	1.00[YRI][hapmap]
rs1177588	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1179947	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1184893	0.81[ASN][1000 genomes]
rs12578258	0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs1375653	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1375654	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1375655	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1630699	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1678952	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1678953	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs1678970	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1720030	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1720068	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1814592	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2009257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2018749	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2272133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272135	0.87[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs2309275	0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4069666	0.86[MEX][hapmap];0.87[TSI][hapmap]
rs483416	0.86[MEX][hapmap];0.87[TSI][hapmap]
rs55929316	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59397548	0.80[AMR][1000 genomes]
rs7309105	0.86[ASW][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs7313748	0.86[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs745327	0.81[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap]
rs830115	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs830121	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1169091	WDR66	cis	cerebellum	SCAN
rs1169091	SUDS3	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122460800-122462600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:122460800-122462600	Enhancers	Fetal Heart	heart
3	chr12:122460800-122463200	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr12:122461000-122462600	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr12:122461200-122462600	Flanking Active TSS	Fetal Thymus	thymus
6	chr12:122461200-122462600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr12:122461600-122462600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:122461600-122462600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:122461600-122466600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:122461600-122467200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:122461600-122492400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:122461800-122464800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:122461800-122465800	Weak transcription	Esophagus	oesophagus
14	chr12:122461800-122473200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:122461800-122476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:122462000-122462600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:122462000-122462600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr12:122462000-122462600	Enhancers	Brain Hippocampus Middle	brain
19	chr12:122462000-122462600	Flanking Active TSS	HSMM	muscle
20	chr12:122462000-122462800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:122462000-122473200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:122462000-122473400	Weak transcription	Primary T cells from cord blood	blood
23	chr12:122462000-122492400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:122462200-122462600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:122462200-122462600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:122462200-122462600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr12:122462200-122462600	Active TSS	Brain Germinal Matrix	brain
28	chr12:122462200-122462600	Enhancers	Colon Smooth Muscle	Colon
29	chr12:122462200-122462600	Enhancers	Fetal Intestine Large	intestine
30	chr12:122462200-122462600	Enhancers	Fetal Intestine Small	intestine
31	chr12:122462200-122462600	Enhancers	Fetal Stomach	stomach
32	chr12:122462200-122462600	Enhancers	Left Ventricle	heart
33	chr12:122462200-122462600	Enhancers	Right Atrium	heart
34	chr12:122462200-122462600	Transcr. at gene 5' and 3'	Thymus	Thymus
35	chr12:122462200-122462600	Enhancers	A549	lung
36	chr12:122462200-122462600	Flanking Active TSS	GM12878-XiMat	blood
37	chr12:122462200-122462600	Enhancers	NH-A	brain
38	chr12:122462200-122462800	Enhancers	Liver	Liver
39	chr12:122462200-122465800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:122462200-122465800	Weak transcription	Psoas Muscle	Psoas
41	chr12:122462200-122466000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:122462200-122466200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:122462200-122466200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:122462200-122466800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:122462200-122469200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:122462200-122469600	Weak transcription	Gastric	stomach
47	chr12:122462200-122472800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:122462200-122473000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr12:122462200-122473200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:122462200-122473400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links