Variant report

Variant	rs7939390
Chromosome Location	chr11:65748249-65748250
allele	A/C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65742158..65748813-chr11:65749011..65756801,11	MCF-7	breast:
2	chr1:156717397..156719936-chr11:65746740..65749009,2	MCF-7	breast:
3	chr11:65628030..65631325-chr11:65748235..65751654,3	MCF-7	breast:
4	chr11:65739309..65741332-chr11:65747619..65750098,2	MCF-7	breast:
5	chr11:65748017..65751656-chr11:65762573..65766422,5	K562	blood:
6	chr11:65747825..65750124-chr11:65778940..65780987,2	MCF-7	breast:
7	chr11:65746618..65749014-chr11:65755089..65756613,2	K562	blood:
8	chr11:65746340..65748696-chr11:65818122..65820186,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172732	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000254867	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000087365	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1047464	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10791835	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10791837	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896070	0.98[ASN][1000 genomes]
rs10896073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10896074	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227370	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12363614	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276132	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759035	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55947178	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60109456	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6591195	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7128076	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs735942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747526	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754532	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7939253	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9735063	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
3	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
5	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
7	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
8	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7939390	BANF1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65730600-65767800	Weak transcription	Right Atrium	heart
2	chr11:65731200-65748600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:65731200-65749600	Strong transcription	Fetal Intestine Small	intestine
4	chr11:65731800-65749000	Strong transcription	Fetal Stomach	stomach
5	chr11:65732400-65748800	Strong transcription	Stomach Smooth Muscle	stomach
6	chr11:65735200-65750600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:65735800-65756600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:65736400-65767400	Weak transcription	Psoas Muscle	Psoas
9	chr11:65737800-65756600	Weak transcription	Stomach Mucosa	stomach
10	chr11:65739200-65749600	Strong transcription	Fetal Brain Female	brain
11	chr11:65739600-65748800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:65739600-65756400	Weak transcription	Fetal Kidney	kidney
13	chr11:65739800-65756400	Weak transcription	Hela-S3	cervix
14	chr11:65741200-65765000	Weak transcription	NHDF-Ad	bronchial
15	chr11:65741400-65762000	Weak transcription	HSMMtube	muscle
16	chr11:65741600-65762000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr11:65742200-65759800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:65743000-65749200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr11:65743000-65749400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:65743800-65764800	Weak transcription	HSMM	muscle
21	chr11:65745000-65764200	Weak transcription	HUVEC	blood vessel
22	chr11:65745200-65764800	Weak transcription	K562	blood
23	chr11:65745400-65750800	Weak transcription	HepG2	liver
24	chr11:65745400-65764800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:65745400-65765000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:65745600-65764200	Weak transcription	NH-A	brain
27	chr11:65745800-65756600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:65745800-65764800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:65746000-65764600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:65746800-65756400	Weak transcription	Brain Substantia Nigra	brain
31	chr11:65746800-65765000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:65747000-65749000	Weak transcription	Brain Anterior Caudate	brain
33	chr11:65747000-65756400	Weak transcription	Primary B cells from cord blood	blood
34	chr11:65747000-65756400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:65747000-65756400	Weak transcription	Aorta	Aorta
36	chr11:65747000-65756400	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:65747000-65764200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr11:65747000-65764600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:65747000-65764600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:65747000-65764600	Weak transcription	Ovary	ovary
41	chr11:65747000-65764800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr11:65747200-65750200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr11:65747200-65750600	Weak transcription	NHLF	lung
44	chr11:65747200-65755600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr11:65747200-65756200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr11:65747200-65756400	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:65747200-65756400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:65747200-65756400	Weak transcription	GM12878-XiMat	blood
49	chr11:65747200-65756600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:65747200-65757200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links