Variant report

Variant	rs9551742
Chromosome Location	chr13:30365783-30365784
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30343717..30345488-chr13:30365364..30367751,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10492458	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11147399	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17625384	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17631187	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278046	0.84[ASN][1000 genomes]
rs278050	0.85[CHD][hapmap]
rs278051	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap]
rs9550497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9550500	1.00[CEU][hapmap]
rs9551735	0.83[EUR][1000 genomes]
rs9551740	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9551746	1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9551747	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
2	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:30341200-30373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:30359000-30367200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr13:30360400-30368000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:30360600-30368000	Weak transcription	Fetal Intestine Large	intestine
7	chr13:30360600-30374800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:30360800-30365800	Weak transcription	Brain Angular Gyrus	brain
9	chr13:30361400-30365800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr13:30361400-30365800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr13:30361400-30367400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:30361800-30373000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr13:30362400-30365800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr13:30362400-30370800	Weak transcription	NHDF-Ad	bronchial
15	chr13:30362400-30375600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:30362600-30372600	Weak transcription	Small Intestine	intestine
17	chr13:30362800-30365800	Weak transcription	Osteobl	bone
18	chr13:30362800-30366800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:30362800-30368400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr13:30363200-30373200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr13:30363400-30368000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:30363400-30372200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:30363400-30375400	Weak transcription	Lung	lung
24	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
25	chr13:30364000-30365800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:30364200-30366200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr13:30364200-30372200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:30364400-30367200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr13:30364600-30365800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr13:30364800-30366600	Enhancers	Brain Hippocampus Middle	brain
31	chr13:30365000-30366000	Enhancers	Gastric	stomach
32	chr13:30365000-30368200	Enhancers	Brain Anterior Caudate	brain
33	chr13:30365000-30373000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr13:30365200-30366200	Enhancers	Stomach Mucosa	stomach
35	chr13:30365200-30370600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr13:30365400-30366000	Enhancers	Liver	Liver
37	chr13:30365400-30366600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr13:30365400-30368000	Enhancers	Brain Substantia Nigra	brain
39	chr13:30365600-30365800	Enhancers	Ovary	ovary
40	chr13:30365600-30366000	Enhancers	Pancreas	Pancrea
41	chr13:30365600-30366200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr13:30365600-30368400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links