Variant report

Variant	rs16923578
Chromosome Location	chr9:5864734-5864735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:5862809..5865732-chr9:5867883..5870745,4	MCF-7	breast:
2	chr9:5864598..5866719-chr9:5878064..5881327,3	MCF-7	breast:
3	chr9:5830855..5833185-chr9:5863294..5866158,2	MCF-7	breast:
4	chr9:5832774..5835758-chr9:5863570..5866452,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099219	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap]
rs10733517	1.00[CEU][hapmap]
rs10733520	1.00[CEU][hapmap]
rs10739079	1.00[CEU][hapmap]
rs10758731	1.00[CEU][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap]
rs1331378	1.00[CEU][hapmap]
rs1331379	1.00[CEU][hapmap]
rs1418740	1.00[CEU][hapmap]
rs1418742	0.94[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs16923551	1.00[AFR][1000 genomes]
rs186913	1.00[CEU][hapmap]
rs2150703	1.00[CEU][hapmap]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap]
rs2291055	1.00[CEU][hapmap]
rs2381360	1.00[CEU][hapmap]
rs343469	1.00[CEU][hapmap]
rs343471	1.00[CEU][hapmap]
rs343480	1.00[CEU][hapmap]
rs343482	1.00[CEU][hapmap]
rs343500	1.00[CEU][hapmap]
rs3739649	1.00[CEU][hapmap]
rs4075225	1.00[CEU][hapmap]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap]
rs4740833	1.00[CEU][hapmap]
rs4742131	1.00[CEU][hapmap]
rs6477010	0.85[ASN][1000 genomes]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap]
rs7029833	1.00[CEU][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap]
rs7034210	1.00[CEU][hapmap]
rs7042947	1.00[CEU][hapmap]
rs7044750	1.00[CEU][hapmap]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017103	chr9:5509431-5987907	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv539965	chr9:5509431-5987907	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv3331803	chr9:5766129-5905103	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv613203	chr9:5841438-5877948	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 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	chr9:5834400-5886000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:5840400-5921600	Weak transcription	Right Ventricle	heart
3	chr9:5840600-5879800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:5844200-5867400	Weak transcription	Adipose Nuclei	Adipose
5	chr9:5844400-5870800	Weak transcription	Lung	lung
6	chr9:5847800-5876200	Weak transcription	Brain Angular Gyrus	brain
7	chr9:5851800-5870600	Weak transcription	Brain Hippocampus Middle	brain
8	chr9:5852200-5873800	Weak transcription	Primary T cells from cord blood	blood
9	chr9:5852200-5897000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:5852400-5878800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:5853800-5875200	Weak transcription	Thymus	Thymus
12	chr9:5853800-5895600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:5854400-5886200	Weak transcription	Brain Anterior Caudate	brain
14	chr9:5854800-5867000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:5855600-5876600	Weak transcription	Fetal Stomach	stomach
16	chr9:5856600-5880000	Weak transcription	Esophagus	oesophagus
17	chr9:5856800-5895600	Weak transcription	Brain Substantia Nigra	brain
18	chr9:5857600-5873200	Weak transcription	Primary B cells from cord blood	blood
19	chr9:5858400-5867400	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:5858600-5876600	Weak transcription	Aorta	Aorta
21	chr9:5858600-5885800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:5859000-5874200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:5859000-5876800	Weak transcription	Left Ventricle	heart
24	chr9:5859000-5895600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:5859000-5906600	Weak transcription	Ovary	ovary
26	chr9:5859200-5867000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:5859200-5919800	Weak transcription	Fetal Brain Female	brain
28	chr9:5859600-5867400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:5859800-5876600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:5862600-5864800	Enhancers	Stomach Mucosa	stomach
31	chr9:5862600-5865000	Enhancers	Duodenum Mucosa	Duodenum
32	chr9:5863400-5864800	Enhancers	Gastric	stomach
33	chr9:5863400-5876800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr9:5863400-5895600	Weak transcription	Fetal Intestine Small	intestine
35	chr9:5863600-5896600	Weak transcription	Pancreas	Pancrea
36	chr9:5863800-5871800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:5864200-5864800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:5864200-5864800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:5864200-5874200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:5864400-5864800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:5864400-5864800	Flanking Active TSS	Hela-S3	cervix
42	chr9:5864400-5869600	Weak transcription	A549	lung
43	chr9:5864400-5869800	Weak transcription	Liver	Liver
44	chr9:5864400-5869800	Weak transcription	HepG2	liver
45	chr9:5864400-5870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:5864400-5872600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:5864600-5864800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr9:5864600-5864800	Enhancers	Spleen	Spleen
49	chr9:5864600-5868800	Weak transcription	Rectal Mucosa Donor 31	rectum

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