Variant report

Variant	rs12516629
Chromosome Location	chr5:179479146-179479147
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179232497..179234437-chr5:179477611..179480495,2	K562	blood:
2	chr5:179478110..179479626-chr5:179490709..179493377,2	K562	blood:
3	chr5:179429959..179431580-chr5:179476627..179479409,2	K562	blood:
4	chr5:179477610..179479379-chr5:179497393..179499345,2	K562	blood:
5	chr5:179477454..179480172-chr5:179480653..179484113,3	MCF-7	breast:
6	chr5:179279889..179282788-chr5:179478192..179480009,2	K562	blood:
7	chr5:179473631..179475664-chr5:179477740..179480217,2	K562	blood:
8	chr5:179474524..179477374-chr5:179479073..179481485,2	MCF-7	breast:
9	chr5:179474733..179479669-chr5:179495487..179500173,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10067073	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs10078845	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10479556	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10479558	1.00[CEU][hapmap]
rs10479559	1.00[CEU][hapmap]
rs10479560	1.00[CEU][hapmap]
rs10516141	1.00[CEU][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes]
rs12514260	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12516233	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12516364	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12516767	1.00[CEU][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13354862	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs13362131	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1345085	1.00[CEU][hapmap]
rs17079941	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs1808088	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4623110	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57144908	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58286692	0.91[AFR][1000 genomes]
rs59150995	0.90[AFR][1000 genomes]
rs60388708	0.92[AFR][1000 genomes]
rs73348268	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73350154	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73350172	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9654545	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers 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 miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers 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 miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
7	chr5:179467400-179483200	Weak transcription	HSMM	muscle
8	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
9	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
10	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
11	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
13	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
14	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
15	chr5:179475200-179481600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr5:179475400-179479400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:179475600-179479200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:179475800-179483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:179476000-179481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:179476000-179484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:179476000-179497800	Weak transcription	Lung	lung
22	chr5:179476200-179479200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:179476400-179481400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:179476400-179486200	Weak transcription	Ovary	ovary
25	chr5:179476400-179487000	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
27	chr5:179476800-179480200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:179477200-179479200	Weak transcription	Fetal Heart	heart
29	chr5:179477200-179480000	Weak transcription	Fetal Lung	lung
30	chr5:179477400-179480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:179477400-179480200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr5:179477400-179481200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:179477400-179483800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr5:179477400-179495000	Weak transcription	Gastric	stomach
36	chr5:179477600-179479200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:179477600-179479200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:179477600-179479200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:179477600-179479200	Weak transcription	K562	blood
40	chr5:179477600-179479800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr5:179477600-179480200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:179477600-179483600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:179477600-179486200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr5:179477800-179479400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr5:179477800-179479400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr5:179477800-179480000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:179477800-179480000	Weak transcription	Liver	Liver
48	chr5:179477800-179481400	Weak transcription	HepG2	liver
49	chr5:179478000-179479600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:179478000-179480000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links