Variant report

Variant	rs11072727
Chromosome Location	chr15:78400311-78400312
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:78251353..78252448-chr15:78400281..78401311,8	MCF-7	breast:
2	chr15:78360788..78361560-chr15:78400133..78400927,2	MCF-7	breast:
3	chr15:78292095..78293104-chr15:78399979..78401592,9	MCF-7	breast:
4	chr15:78258802..78259810-chr15:78400203..78401702,8	MCF-7	breast:
5	chr15:78394209..78398078-chr15:78398123..78400882,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78400089-78400752	l_1195_chr15:78344341-78421177_testes

No data

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10456	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11072728	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639461	0.84[ASN][1000 genomes]
rs2304828	0.81[ASN][1000 genomes]
rs2304829	0.91[ASN][1000 genomes]
rs2867922	0.84[ASN][1000 genomes]
rs59999498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62009267	0.84[ASN][1000 genomes]
rs62009270	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009271	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6495273	0.87[ASN][1000 genomes]
rs7162025	0.87[ASN][1000 genomes]
rs7164338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72732564	0.84[ASN][1000 genomes]
rs8028859	0.87[ASN][1000 genomes]
rs8032449	0.90[ASN][1000 genomes]
rs9806257	0.84[EUR][1000 genomes];0.94[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv274890	chr15:78396447-78402258	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11072727	CIB2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78385200-78400600	Weak transcription	Pancreas	Pancrea
2	chr15:78392000-78400600	Strong transcription	Thymus	Thymus
3	chr15:78393200-78406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78393400-78401200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:78395000-78405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:78395400-78405600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:78396000-78405400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78396200-78400600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr15:78396200-78400600	Weak transcription	Right Atrium	heart
10	chr15:78396200-78405600	Weak transcription	Brain Anterior Caudate	brain
11	chr15:78396200-78421800	Weak transcription	Right Ventricle	heart
12	chr15:78396400-78404000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:78396400-78405400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:78396600-78405400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:78396600-78405600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:78396600-78423800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:78396800-78401400	Strong transcription	Fetal Stomach	stomach
18	chr15:78397000-78400600	Weak transcription	Fetal Lung	lung
19	chr15:78397000-78405600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:78397200-78400600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr15:78397600-78400600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr15:78397600-78401200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:78397600-78421400	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:78398400-78405400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:78398400-78405600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:78398400-78423200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:78398600-78400400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:78398600-78400600	Strong transcription	Fetal Thymus	thymus
29	chr15:78398600-78400600	Weak transcription	Osteobl	bone
30	chr15:78398600-78400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:78398600-78405200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:78398600-78405600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:78398600-78413200	Weak transcription	Spleen	Spleen
34	chr15:78398800-78400400	Weak transcription	HSMMtube	muscle
35	chr15:78398800-78400600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:78398800-78400600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:78398800-78400600	Weak transcription	Stomach Mucosa	stomach
38	chr15:78398800-78400800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:78398800-78406200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:78399000-78400600	Strong transcription	Fetal Intestine Large	intestine
41	chr15:78399000-78400600	Weak transcription	GM12878-XiMat	blood
42	chr15:78399000-78402000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:78399000-78405400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:78399200-78400600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:78399200-78400600	Strong transcription	Fetal Intestine Small	intestine
46	chr15:78399600-78401200	Enhancers	Placenta	Placenta
47	chr15:78399800-78400800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr15:78400000-78400400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:78400000-78400600	Weak transcription	HepG2	liver
50	chr15:78400000-78400800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links