Variant report

Variant	rs16929541
Chromosome Location	chr9:12790687-12790688
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:12773433..12781932-chr9:12782481..12798090,47	MCF-7	breast:
2	chr9:12774109..12791345-chr9:12812800..12822770,37	MCF-7	breast:
3	chr9:12788809..12790728-chr9:12792217..12794767,4	MCF-7	breast:
4	chr9:12789292..12791495-chr9:12794969..12797067,2	MCF-7	breast:
5	chr9:5854256..5856803-chr9:12790614..12793175,2	MCF-7	breast:
6	chr9:12773969..12780098-chr9:12789328..12796142,13	MCF-7	breast:
7	chr9:12729225..12731478-chr9:12790178..12792905,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPDZ-1	chr9:12790619-12790764	ENSG00000235448.1

No data

Variant related genes	Relation type
ENSG00000235448	Chromatin interaction
ENSG00000223621	Chromatin interaction
ENSG00000153714	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17346161	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12785400-12808800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:12785800-12791200	Weak transcription	HepG2	liver
3	chr9:12785800-12791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:12785800-12797200	Weak transcription	Aorta	Aorta
5	chr9:12785800-12798200	Weak transcription	HSMMtube	muscle
6	chr9:12785800-12802200	Weak transcription	Left Ventricle	heart
7	chr9:12785800-12813600	Weak transcription	Fetal Intestine Large	intestine
8	chr9:12786000-12791000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:12786000-12791400	Weak transcription	Fetal Stomach	stomach
10	chr9:12786000-12793400	Weak transcription	Stomach Mucosa	stomach
11	chr9:12786000-12797000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:12786000-12813600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:12786000-12813600	Weak transcription	Fetal Intestine Small	intestine
14	chr9:12786400-12798400	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:12787000-12796800	Weak transcription	NHEK	skin
16	chr9:12789000-12794000	Enhancers	Osteobl	bone
17	chr9:12789200-12791000	Enhancers	A549	lung
18	chr9:12789200-12791200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:12789200-12798600	Enhancers	NHDF-Ad	bronchial
20	chr9:12789400-12792000	Enhancers	Adipose Nuclei	Adipose
21	chr9:12789400-12793000	Enhancers	Fetal Lung	lung
22	chr9:12789400-12793200	Enhancers	NHLF	lung
23	chr9:12789600-12791200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:12789800-12791000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:12789800-12793600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:12790000-12791000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr9:12790000-12791200	Enhancers	Rectal Smooth Muscle	rectum
28	chr9:12790000-12793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr9:12790200-12791200	Enhancers	Colon Smooth Muscle	Colon
30	chr9:12790400-12791000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:12790400-12791000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:12790400-12791200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:12790400-12791800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:12790400-12792000	Weak transcription	Hela-S3	cervix
35	chr9:12790400-12793400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr9:12790400-12796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:12790600-12791800	Weak transcription	Fetal Kidney	kidney

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