Variant report

Variant	rs11204752
Chromosome Location	chr1:150958133-150958134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150955685..150958316-chr1:150971116..150974033,3	MCF-7	breast:
2	chr1:150949558..150951518-chr1:150957213..150958786,2	K562	blood:
3	chr1:150952248..150956266-chr1:150957653..150962515,6	K562	blood:
4	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143363	Chromatin interaction
ENSG00000143412	Chromatin interaction
ENSG00000143409	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11204754	0.81[AFR][1000 genomes]
rs11587718	0.90[ASN][1000 genomes]
rs11587720	0.92[ASN][1000 genomes]
rs1673160	0.91[ASN][1000 genomes]
rs2305814	0.98[ASN][1000 genomes]
rs267735	0.85[ASN][1000 genomes]
rs3754211	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4970932	0.81[ASN][1000 genomes]
rs6587551	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs771201	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11204752	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204752	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204752	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204752	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204752	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11204752	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204752	RP11-316M1.12	cis	Artery Tibial	GTEx
rs11204752	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204752	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs11204752	RP11-316M1.12	cis	Thyroid	GTEx
rs11204752	RP11-316M1.12	cis	lung	GTEx
rs11204752	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11204752	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs11204752	ENSA	Cis_1M	lymphoblastoid	RTeQTL
rs11204752	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204752	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
2	chr1:150952600-150960800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:150952600-150968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:150953600-150959000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:150954200-150969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:150954800-150968000	Weak transcription	Fetal Kidney	kidney
7	chr1:150955000-150969400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:150955400-150969400	Weak transcription	Gastric	stomach
9	chr1:150955400-150970400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:150955400-150978800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:150955600-150967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:150955600-150968200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:150955800-150967600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:150956200-150958600	Weak transcription	Liver	Liver
15	chr1:150956200-150969400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:150956600-150958200	Enhancers	Pancreas	Pancrea
17	chr1:150957400-150958400	Enhancers	Hela-S3	cervix
18	chr1:150957600-150958200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:150957600-150958400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:150957800-150958200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:150957800-150958400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:150957800-150958800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:150957800-150967600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:150958000-150958200	Weak transcription	K562	blood
25	chr1:150958000-150958600	Weak transcription	HepG2	liver
26	chr1:150958000-150967600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links