Variant report

Variant	rs12346677
Chromosome Location	chr9:110249962-110249963
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:110247849..110250590-chr9:111329415..111332131,3	MCF-7	breast:
2	chr9:110248541..110250333-chr9:110285200..110286705,2	MCF-7	breast:
3	chr9:110190788..110193642-chr9:110249721..110252458,4	MCF-7	breast:
4	chr9:110184199..110185540-chr9:110249535..110250385,9	MCF-7	breast:
5	chr9:110248220..110250527-chr9:111302470..111304423,3	MCF-7	breast:
6	chr9:109425556..109427280-chr9:110248781..110250709,2	MCF-7	breast:
7	chr6:27114514..27116900-chr9:110249066..110251372,2	MCF-7	breast:
8	chr9:110184526..110185075-chr9:110249421..110250069,3	MCF-7	breast:
9	chr9:110248605..110250352-chr9:110763897..110765598,2	MCF-7	breast:
10	chr9:110189538..110195123-chr9:110249494..110254933,10	MCF-7	breast:
11	chr9:110246769..110253919-chr9:110298442..110306182,20	MCF-7	breast:
12	chr9:110249421..110250120-chr9:110279381..110280253,2	MCF-7	breast:
13	chr9:110242425..110245039-chr9:110248076..110250038,3	K562	blood:
14	chr9:110185127..110185629-chr9:110249513..110250083,2	MCF-7	breast:
15	chr9:110248818..110250564-chr9:110802870..110804460,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000227350	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000234229	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000226825	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11573728	1.00[CHD][hapmap]

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	nsv530948	chr9:109760752-110413602	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv825028	chr9:110248596-110252543	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:110244000-110250400	Weak transcription	HSMMtube	muscle
2	chr9:110246200-110253800	Active TSS	Right Atrium	heart
3	chr9:110247000-110250600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:110247200-110250000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:110247200-110250400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
6	chr9:110247200-110250600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:110247200-110250800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:110247200-110254000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr9:110247400-110251400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
10	chr9:110247400-110253800	Active TSS	Psoas Muscle	Psoas
11	chr9:110247600-110250400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
12	chr9:110247600-110250600	Active TSS	Brain Hippocampus Middle	brain
13	chr9:110247600-110250600	Active TSS	Small Intestine	intestine
14	chr9:110247600-110250600	Transcr. at gene 5' and 3'	NHLF	lung
15	chr9:110248000-110250800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:110248200-110250400	Weak transcription	Aorta	Aorta
17	chr9:110248400-110250000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:110248400-110254200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr9:110248600-110250800	Transcr. at gene 5' and 3'	Sigmoid Colon	Sigmoid Colon
20	chr9:110248600-110252800	Active TSS	Brain Cingulate Gyrus	brain
21	chr9:110248800-110250200	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
22	chr9:110249000-110250000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:110249000-110250000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
24	chr9:110249000-110250200	Transcr. at gene 5' and 3'	Ovary	ovary
25	chr9:110249000-110250400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:110249000-110250800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
27	chr9:110249000-110251000	Transcr. at gene 5' and 3'	Esophagus	oesophagus
28	chr9:110249000-110251000	Transcr. at gene 5' and 3'	Lung	lung
29	chr9:110249000-110251000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
30	chr9:110249000-110251600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr9:110249000-110251800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr9:110249000-110251800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
33	chr9:110249000-110251800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr9:110249000-110252600	Active TSS	Osteobl	bone
35	chr9:110249000-110253200	Active TSS	Brain Substantia Nigra	brain
36	chr9:110249000-110253800	Active TSS	Brain Anterior Caudate	brain
37	chr9:110249200-110250000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:110249200-110250000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:110249200-110250000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr9:110249200-110250000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:110249200-110250200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
42	chr9:110249200-110250200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:110249200-110250200	Transcr. at gene 5' and 3'	Spleen	Spleen
44	chr9:110249200-110251200	Transcr. at gene 5' and 3'	Gastric	stomach
45	chr9:110249200-110251400	Bivalent/Poised TSS	Fetal Kidney	kidney
46	chr9:110249200-110251600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
47	chr9:110249200-110251600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
48	chr9:110249200-110253000	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr9:110249200-110253400	Active TSS	Brain Angular Gyrus	brain
50	chr9:110249200-110254200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links