Variant report

Variant	rs11542163
Chromosome Location	chr6:36887476-36887477
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36886112..36887958-chr6:36978149..36979897,2	MCF-7	breast:
2	chr6:36879267..36882648-chr6:36885620..36888336,3	K562	blood:
3	chr6:36885661..36888291-chr6:36984443..36986353,2	MCF-7	breast:
4	chr6:36885599..36889594-chr6:36935719..36938209,3	MCF-7	breast:
5	chr6:36743912..36745696-chr6:36885274..36887622,2	K562	blood:
6	chr6:36884368..36885933-chr6:36886588..36889319,2	K562	blood:
7	chr6:36885468..36888392-chr6:36943726..36946366,2	MCF-7	breast:
8	chr6:36884977..36888283-chr6:36895013..36898238,3	K562	blood:
9	chr6:36883006..36885868-chr6:36886588..36888530,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11751310	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751956	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753183	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11753835	0.91[EUR][1000 genomes]
rs11757851	0.92[EUR][1000 genomes]
rs11759158	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11759163	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12660916	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660989	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191679	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13200132	1.00[ASN][1000 genomes]
rs13205108	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13205292	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206310	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207209	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210299	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17552005	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34405617	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34433592	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34510528	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34597881	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34869908	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34913693	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35819257	0.95[EUR][1000 genomes]
rs36098393	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569352	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71569356	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470425	0.88[EUR][1000 genomes];1.00[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	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11542163	C6orf89	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36854400-36893000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:36866200-36896400	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:36867000-36897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:36870800-36889400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:36871000-36888400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:36877800-36896000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:36879400-36894000	Strong transcription	Fetal Brain Female	brain
8	chr6:36879600-36894000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:36879600-36895400	Strong transcription	Brain Germinal Matrix	brain
10	chr6:36880000-36892000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr6:36880200-36887800	Strong transcription	Adipose Nuclei	Adipose
12	chr6:36880200-36893800	Strong transcription	K562	blood
13	chr6:36880400-36888000	Strong transcription	Brain Angular Gyrus	brain
14	chr6:36880600-36893600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr6:36880600-36900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:36880800-36889800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr6:36881000-36892000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:36881000-36894800	Weak transcription	Fetal Brain Male	brain
19	chr6:36881200-36889600	Strong transcription	Brain Hippocampus Middle	brain
20	chr6:36881400-36893000	Strong transcription	Spleen	Spleen
21	chr6:36881400-36893600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:36881400-36893800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:36881400-36896200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:36881600-36889600	Strong transcription	Brain Cingulate Gyrus	brain
25	chr6:36881600-36891200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:36882000-36891600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:36882000-36893800	Strong transcription	Liver	Liver
28	chr6:36882200-36889200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr6:36882200-36891000	Strong transcription	Thymus	Thymus
30	chr6:36882200-36892000	Strong transcription	Brain Anterior Caudate	brain
31	chr6:36882200-36894000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:36882400-36891200	Weak transcription	HUVEC	blood vessel
33	chr6:36882400-36891800	Strong transcription	Primary T cells from cord blood	blood
34	chr6:36882400-36893000	Strong transcription	Fetal Intestine Large	intestine
35	chr6:36882400-36893600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:36882400-36893800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr6:36882400-36894800	Strong transcription	Fetal Intestine Small	intestine
38	chr6:36882400-36895600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:36882400-36896800	Weak transcription	Hela-S3	cervix
40	chr6:36882600-36889800	Strong transcription	Primary B cells from cord blood	blood
41	chr6:36882600-36893800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:36882600-36893800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:36882600-36893800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:36882600-36894000	Strong transcription	Dnd41	blood
45	chr6:36882800-36887600	Weak transcription	NHEK	skin
46	chr6:36882800-36889400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr6:36882800-36891400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr6:36882800-36892800	Weak transcription	Fetal Kidney	kidney
49	chr6:36882800-36893800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:36883000-36893600	Weak transcription	A549	lung

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