Variant report

Variant	rs7122539
Chromosome Location	chr11:66662731-66662732
allele	A/G
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	chr11:66660192..66664541-chr11:66668584..66671448,3	K562	blood:
2	chr11:66661036..66663353-chr11:66724438..66726051,2	MCF-7	breast:
3	chr11:66655145..66657137-chr11:66660875..66665067,4	K562	blood:
4	chr11:66660543..66663363-chr11:66674635..66676810,3	MCF-7	breast:
5	chr11:66657847..66661225-chr11:66662728..66665638,3	K562	blood:
6	chr11:66656177..66657734-chr11:66661221..66662928,2	MCF-7	breast:
7	chr11:66661590..66663359-chr11:66761775..66763735,2	MCF-7	breast:
8	chr11:66622922..66625228-chr11:66660232..66663012,2	MCF-7	breast:
9	chr11:66661363..66663276-chr11:66678554..66680606,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252709	Chromatin interaction
ENSG00000173621	Chromatin interaction
ENSG00000173599	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10160758	0.88[TSI][hapmap]
rs10896139	0.86[TSI][hapmap]
rs11600959	0.81[TSI][hapmap]
rs2077432	0.83[TSI][hapmap]
rs2167457	0.83[TSI][hapmap]
rs2187041	0.83[TSI][hapmap]
rs4008953	0.89[AFR][1000 genomes]
rs6591222	0.83[ASW][hapmap]
rs6591223	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7119426	0.86[TSI][hapmap]
rs7120256	0.83[TSI][hapmap]
rs7931485	0.86[EUR][1000 genomes]
rs7948839	0.88[TSI][hapmap]

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	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HIV-1 susceptibility	22174851	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7122539	ENSG00000173621	cis	multi-tissue	Pritchard
rs7122539	B3GNT1	cis	parietal	SCAN
rs7122539	PC	cis	cerebellum	SCAN
rs7122539	KDM2A	cis	cerebellum	SCAN
rs7122539	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs7122539	EHBP1L1	cis	cerebellum	SCAN
rs7122539	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs7122539	B3GNT1	cis	cerebellum	SCAN
rs7122539	LRFN4	cis	lymphoblastoid	seeQTL
rs7122539	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66651000-66664000	Weak transcription	Right Ventricle	heart
2	chr11:66651200-66665600	Weak transcription	Brain Germinal Matrix	brain
3	chr11:66651200-66669800	Weak transcription	Fetal Intestine Small	intestine
4	chr11:66651200-66673200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:66651400-66678400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:66654600-66673800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:66656200-66668600	Weak transcription	Liver	Liver
8	chr11:66660000-66663400	Weak transcription	Adipose Nuclei	Adipose
9	chr11:66660000-66672200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:66660200-66665400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:66660200-66673600	Weak transcription	HSMMtube	muscle
12	chr11:66660600-66665200	Weak transcription	HepG2	liver
13	chr11:66660600-66673600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:66660800-66665000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:66660800-66668800	Weak transcription	Brain Anterior Caudate	brain
16	chr11:66660800-66671600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:66660800-66671600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:66660800-66672600	Weak transcription	Psoas Muscle	Psoas
19	chr11:66661000-66662800	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:66661000-66664000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:66661000-66668400	Weak transcription	NHEK	skin
22	chr11:66661000-66669200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:66661200-66669600	Weak transcription	HMEC	breast
24	chr11:66661400-66662800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:66661600-66664000	Weak transcription	Hela-S3	cervix
26	chr11:66661600-66665400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:66661800-66670600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:66662000-66665200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr11:66662200-66662800	Enhancers	Esophagus	oesophagus
30	chr11:66662200-66663800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:66662200-66663800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:66662200-66673600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:66662400-66662800	Weak transcription	A549	lung

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