Variant report

Variant	rs6590967
Chromosome Location	chr11:102364985-102364986
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:102216583..102219205-chr11:102364748..102366652,2	MCF-7	breast:
2	chr11:102358831..102361253-chr11:102363171..102365874,2	MCF-7	breast:
3	chr11:102217635..102219637-chr11:102364748..102366957,2	K562	blood:
4	chr11:102323470..102325107-chr11:102364367..102365927,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152558	Chromatin interaction
ENSG00000110330	Chromatin interaction
ENSG00000255337	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10750642	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10750643	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10791576	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1941510	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2186992	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2850437	0.91[ASN][1000 genomes]
rs3990027	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4754045	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs488324	0.93[ASN][1000 genomes]
rs514188	0.93[ASN][1000 genomes]
rs555650	0.97[ASN][1000 genomes]
rs562383	0.92[ASN][1000 genomes]
rs599384	0.91[ASN][1000 genomes]
rs603608	0.97[ASN][1000 genomes]
rs634743	0.92[ASN][1000 genomes]
rs634814	0.93[ASN][1000 genomes]
rs636898	0.92[ASN][1000 genomes]
rs650423	0.92[ASN][1000 genomes]
rs651319	0.92[ASN][1000 genomes]
rs653586	0.99[ASN][1000 genomes]
rs6590964	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6590966	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs659789	0.90[ASN][1000 genomes]
rs665124	0.99[ASN][1000 genomes]
rs668660	0.98[ASN][1000 genomes]
rs938598	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs938600	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	nsv1035567	chr11:102264516-102431607	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv469990	chr11:102335609-102413943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv556150	chr11:102335609-102415859	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv468854	chr11:102336617-102413943	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv556151	chr11:102336617-102413943	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6590967	TMEM123	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:102358400-102365600	Weak transcription	Primary T cells from cord blood	blood
2	chr11:102363600-102366400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:102364000-102365200	Weak transcription	GM12878-XiMat	blood
4	chr11:102364200-102365200	Enhancers	Fetal Intestine Large	intestine
5	chr11:102364200-102365800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:102364200-102366800	Enhancers	Liver	Liver
7	chr11:102364400-102365000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:102364400-102365000	Enhancers	Duodenum Mucosa	Duodenum
9	chr11:102364400-102365000	Weak transcription	Fetal Intestine Small	intestine
10	chr11:102364400-102365200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:102364400-102366200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:102364400-102366200	Enhancers	HMEC	breast
13	chr11:102364400-102366400	Enhancers	NHEK	skin
14	chr11:102364400-102366800	Enhancers	Hela-S3	cervix
15	chr11:102364600-102365000	Enhancers	HepG2	liver
16	chr11:102364600-102365600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:102364600-102365600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr11:102364600-102366200	Enhancers	HUVEC	blood vessel
19	chr11:102364800-102365400	Active TSS	A549	lung
20	chr11:102364800-102365600	Weak transcription	Stomach Mucosa	stomach
21	chr11:102364800-102366600	Enhancers	Muscle Satellite Cultured Cells	--

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