Variant report

Variant	rs11204853
Chromosome Location	chr1:151557131-151557132
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151511523..151514176-chr1:151553602..151559967,11	MCF-7	breast:
2	1:151478607-151483211..1:151554759-151560153	Hela-S3	cervix:
3	chr1:151517397..151520061-chr1:151554421..151557663,3	MCF-7	breast:
4	chr1:151556789..151559689-chr1:151565337..151567125,2	MCF-7	breast:
5	chr1:151555489..151558097-chr1:151879196..151882038,2	MCF-7	breast:
6	1:151496437-151509688..1:151554759-151560153	Hela-S3	cervix:
7	chr1:151518179..151521710-chr1:151554495..151558712,6	MCF-7	breast:
8	chr1:151554350..151557828-chr1:151561195..151563767,4	K562	blood:
9	1:151554759-151560153..1:151618750-151636526	Hela-S3	cervix:
10	1:151411623-151426875..1:151554759-151560153	Hela-S3	cervix:
11	chr1:151539684..151544323-chr1:151552691..151557234,8	MCF-7	breast:
12	chr1:151539929..151545457-chr1:151553538..151558687,9	MCF-7	breast:
13	chr1:151556628..151559025-chr1:151567592..151570969,4	MCF-7	breast:
14	1:151516085-151535167..1:151554759-151560153	Hela-S3	cervix:
15	chr1:151512630..151515300-chr1:151556777..151558528,2	MCF-7	breast:
16	chr1:151555396..151557828-chr1:151561195..151563798,3	K562	blood:
17	chr1:151553312..151555156-chr1:151556818..151558508,3	MCF-7	breast:
18	chr1:151546253..151548190-chr1:151557087..151559275,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143375	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11204850	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11204854	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11204856	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1196346	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs1196348	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs1196349	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1196351	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs1196356	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1196463	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs12031503	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12409434	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1308135	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs1308142	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs1308149	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1308151	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs1308153	0.81[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs1308155	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1308156	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap]
rs1781432	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2495395	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap]
rs2997072	1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs3790505	0.89[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4845778	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs60393350	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151521800-151559000	Weak transcription	Small Intestine	intestine
2	chr1:151533000-151557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:151533800-151561600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:151535800-151561800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:151537400-151558400	Weak transcription	Fetal Kidney	kidney
6	chr1:151538000-151557400	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:151542600-151557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:151548000-151557200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:151548400-151557400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:151548800-151557200	Strong transcription	Brain Germinal Matrix	brain
11	chr1:151548800-151558200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:151550400-151559800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:151550800-151557600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:151551800-151557800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:151552400-151558200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:151552600-151557200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:151552600-151559800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:151552800-151557200	Weak transcription	Brain Anterior Caudate	brain
19	chr1:151552800-151558000	Weak transcription	Hela-S3	cervix
20	chr1:151553200-151557400	Genic enhancers	HSMMtube	muscle
21	chr1:151553800-151558200	Weak transcription	NHLF	lung
22	chr1:151554000-151557400	Genic enhancers	NHEK	skin
23	chr1:151554400-151560000	Weak transcription	Fetal Brain Female	brain
24	chr1:151554800-151557400	Weak transcription	Gastric	stomach
25	chr1:151554800-151558000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:151554800-151558000	Weak transcription	Aorta	Aorta
27	chr1:151554800-151559200	Weak transcription	HepG2	liver
28	chr1:151554800-151559800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:151554800-151560000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:151554800-151566200	Weak transcription	Ovary	ovary
31	chr1:151555000-151558000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:151555000-151558400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:151555000-151558800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:151555000-151560200	Enhancers	Placenta	Placenta
35	chr1:151555000-151568800	Weak transcription	Liver	Liver
36	chr1:151555200-151559800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:151555200-151559800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:151555400-151558000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:151555400-151558000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr1:151555400-151580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:151555600-151566600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:151555800-151557400	Genic enhancers	HSMM	muscle
43	chr1:151556000-151557200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:151556000-151558600	Enhancers	Adipose Nuclei	Adipose
45	chr1:151556000-151558800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr1:151556200-151557200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:151556200-151557200	Genic enhancers	A549	lung
48	chr1:151556200-151557600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:151556200-151557800	Enhancers	Esophagus	oesophagus
50	chr1:151556200-151557800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links