Variant report

Variant	rs1089468
Chromosome Location	chr7:86952399-86952400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:86945551..86947910-chr7:86951997..86954266,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28381964	1.00[AMR][1000 genomes]
rs73707354	1.00[AMR][1000 genomes]
rs802049	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs802050	0.83[AFR][1000 genomes]
rs802051	1.00[YRI][hapmap];0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025277	chr7:86299224-87206007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv538999	chr7:86299224-87206007	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv532147	chr7:86299225-87121975	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv888677	chr7:86802025-87781111	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv464622	chr7:86832603-87541248	Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv607725	chr7:86832603-87541248	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1029486	chr7:86856387-87121976	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv539004	chr7:86856387-87121976	Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	esv1814401	chr7:86857553-87034167	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
10	esv1826474	chr7:86857553-87034167	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv428177	chr7:86857553-87034167	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	esv1828294	chr7:86857553-87147397	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv1024376	chr7:86905796-87129346	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv1026153	chr7:86905796-87258822	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	nsv1022111	chr7:86918603-86966719	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv888678	chr7:86932085-87101407	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
17	esv1791762	chr7:86940803-86954233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:86940600-86956400	Weak transcription	Fetal Intestine Large	intestine
2	chr7:86944800-86952400	Weak transcription	Pancreas	Pancrea
3	chr7:86946800-86954800	Weak transcription	Fetal Muscle Leg	muscle
4	chr7:86946800-86956400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr7:86947200-86954800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr7:86948400-86952400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:86948600-86952400	Weak transcription	Lung	lung
8	chr7:86948600-86955400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr7:86948600-86956800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:86948800-86952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:86948800-86952400	Weak transcription	Liver	Liver
12	chr7:86948800-86952400	Weak transcription	Esophagus	oesophagus
13	chr7:86948800-86952400	Weak transcription	Left Ventricle	heart
14	chr7:86948800-86952400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:86948800-86953400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:86948800-86953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:86948800-86956000	Weak transcription	Right Ventricle	heart
18	chr7:86948800-86956200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:86948800-86956200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:86948800-86956200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr7:86948800-86956400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:86949000-86952400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr7:86949000-86952400	Weak transcription	Primary T cells from cord blood	blood
24	chr7:86949000-86952400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:86949000-86953200	Weak transcription	Stomach Mucosa	stomach
26	chr7:86949000-86953600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:86949000-86956000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr7:86949000-86956200	Weak transcription	Colonic Mucosa	Colon
29	chr7:86949000-86956400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:86949000-86956400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr7:86949000-86956600	Weak transcription	Colon Smooth Muscle	Colon
32	chr7:86949000-86956800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr7:86949000-86957000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr7:86949000-86957600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:86949400-86957600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:86950600-86952400	Weak transcription	Ovary	ovary
37	chr7:86950800-86956000	Weak transcription	Aorta	Aorta
38	chr7:86951000-86972600	Weak transcription	Fetal Kidney	kidney
39	chr7:86951800-86953200	Enhancers	HMEC	breast
40	chr7:86952000-86960600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr7:86952000-86962000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:86952200-86952600	ZNF genes & repeats	Adipose Nuclei	Adipose
43	chr7:86952200-86952800	ZNF genes & repeats	Brain Hippocampus Middle	brain
44	chr7:86952200-86953000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:86952200-86953000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
46	chr7:86952200-86953000	Enhancers	NHEK	skin
47	chr7:86952200-86953200	Enhancers	Placenta	Placenta
48	chr7:86952200-86954200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:86952200-86954800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links