Variant report

Variant	rs10125581
Chromosome Location	chr9:12783350-12783351
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:12783262..12785196-chr9:12857512..12860310,2	MCF-7	breast:
2	chr9:12773433..12781932-chr9:12782481..12798090,47	MCF-7	breast:
3	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
4	chr9:12773974..12784053-chr9:12813051..12820453,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235448	Chromatin interaction
ENSG00000153714	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10756411	0.84[ASN][1000 genomes]
rs10756412	0.84[ASN][1000 genomes]
rs10756413	0.84[ASN][1000 genomes]
rs10809839	0.86[ASN][1000 genomes]
rs10809840	0.86[ASN][1000 genomes]
rs10809841	0.83[ASN][1000 genomes]
rs10809842	0.86[ASN][1000 genomes]
rs10809845	0.84[EUR][1000 genomes]
rs10960792	0.85[ASN][1000 genomes]
rs1326800	0.86[ASN][1000 genomes]
rs7468492	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1030835	chr9:12717405-12840928	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv892573	chr9:12730636-12874703	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv892574	chr9:12754969-12918226	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12776800-12784400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:12777000-12784000	Weak transcription	Stomach Mucosa	stomach
3	chr9:12777000-12784200	Weak transcription	Small Intestine	intestine
4	chr9:12777000-12784200	Weak transcription	K562	blood
5	chr9:12777000-12784400	Weak transcription	HUVEC	blood vessel
6	chr9:12777000-12784600	Weak transcription	Left Ventricle	heart
7	chr9:12777000-12784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:12777200-12784000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:12777400-12785000	Weak transcription	Lung	lung
10	chr9:12778200-12784400	Weak transcription	Placenta	Placenta
11	chr9:12778400-12784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:12778400-12784600	Weak transcription	Pancreas	Pancrea
13	chr9:12778400-12785000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:12778400-12785000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:12778400-12785200	Weak transcription	Ovary	ovary
16	chr9:12778600-12783800	Weak transcription	HMEC	breast
17	chr9:12778600-12785400	Weak transcription	Liver	Liver
18	chr9:12778800-12783400	Weak transcription	HSMMtube	muscle
19	chr9:12778800-12784000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:12778800-12784200	Weak transcription	Fetal Stomach	stomach
21	chr9:12779000-12783600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:12779000-12784000	Weak transcription	NHEK	skin
23	chr9:12779000-12784200	Weak transcription	Fetal Intestine Small	intestine
24	chr9:12779000-12785000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:12779200-12785400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:12780000-12785000	Weak transcription	Right Atrium	heart
27	chr9:12780200-12784200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:12780400-12783400	Weak transcription	Hela-S3	cervix
29	chr9:12780400-12784800	Weak transcription	Brain Substantia Nigra	brain
30	chr9:12780400-12785000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:12781400-12783400	ZNF genes & repeats	A549	lung
32	chr9:12781400-12783600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:12781400-12783800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:12781400-12783800	ZNF genes & repeats	Fetal Lung	lung
35	chr9:12781800-12783600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr9:12781800-12784000	Weak transcription	NHLF	lung
37	chr9:12781800-12784200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:12781800-12784200	Weak transcription	Osteobl	bone
39	chr9:12781800-12784400	Weak transcription	Adipose Nuclei	Adipose
40	chr9:12782000-12783600	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:12782000-12784200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr9:12782200-12783400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:12782400-12783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:12782400-12784200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:12782400-12785000	Weak transcription	Aorta	Aorta
46	chr9:12782600-12784600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:12782800-12783600	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links