Variant report

Variant	rs11576129
Chromosome Location	chr1:185534994-185534995
allele	A/C
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	NFIC	chr1:185534299-185535019	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr1:185534302-185535078	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr1:185534155-185535012	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr1:185534284-185535008	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185534952..185537044-chr1:185538888..185541072,3	MCF-7	breast:
2	chr1:185284868..185287511-chr1:185534304..185536690,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228309	TF binding region
ENSG00000273004	Chromatin interaction
ENSG00000116679	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10911754	0.84[EUR][1000 genomes]
rs10911755	0.84[EUR][1000 genomes]
rs10911756	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11576884	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11581960	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583193	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586588	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11586605	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12029108	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12046138	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12048982	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402146	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12402607	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1321998	0.84[EUR][1000 genomes]
rs1321999	0.84[EUR][1000 genomes]
rs2295792	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28776539	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35495151	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41453048	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56164019	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56822355	0.85[EUR][1000 genomes]
rs57836721	0.84[EUR][1000 genomes]
rs58848006	0.84[EUR][1000 genomes]
rs6701720	0.80[ASN][1000 genomes]
rs72726098	0.84[EUR][1000 genomes]
rs72727706	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72727712	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72727717	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72727728	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74132957	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7518777	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548398	chr1:185136458-186003094	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185525400-185536000	Weak transcription	Stomach Mucosa	stomach
2	chr1:185528000-185536000	Weak transcription	Fetal Kidney	kidney
3	chr1:185528600-185539800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:185529200-185535400	Weak transcription	Small Intestine	intestine
5	chr1:185529400-185543000	Weak transcription	Pancreas	Pancrea
6	chr1:185529600-185535800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:185530400-185535000	Weak transcription	Primary B cells from cord blood	blood
8	chr1:185530400-185535400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:185530400-185536000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:185530800-185535800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:185530800-185536600	Weak transcription	Left Ventricle	heart
12	chr1:185530800-185544000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:185531000-185535200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:185531000-185535800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr1:185531200-185536000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:185531800-185540400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:185532200-185536200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:185532800-185538800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:185533000-185535800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr1:185533000-185538800	Enhancers	HMEC	breast
21	chr1:185533000-185540200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:185533000-185540800	Enhancers	NHEK	skin
23	chr1:185533200-185535800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr1:185533200-185536000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:185533400-185536000	Enhancers	Primary T cells from cord blood	blood
26	chr1:185533400-185539000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:185533600-185536000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:185533600-185536400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:185533800-185535000	Enhancers	Placenta	Placenta
30	chr1:185533800-185535000	Enhancers	NH-A	brain
31	chr1:185533800-185536400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:185534000-185535000	Enhancers	Hela-S3	cervix
33	chr1:185534000-185536000	Enhancers	Thymus	Thymus
34	chr1:185534000-185537000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:185534000-185537200	Enhancers	Fetal Heart	heart
36	chr1:185534200-185537800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:185534200-185540000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:185534400-185536000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:185534400-185536000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:185534400-185536200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr1:185534400-185536400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:185534400-185538800	Enhancers	Primary hematopoietic stem cells	blood
43	chr1:185534600-185535000	Enhancers	HSMMtube	muscle
44	chr1:185534600-185535800	Enhancers	Fetal Thymus	thymus
45	chr1:185534600-185536000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr1:185534600-185538600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr1:185534600-185540200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr1:185534800-185535200	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:185534800-185535400	Weak transcription	Gastric	stomach
50	chr1:185534800-185535800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links