Variant report

Variant	rs13435998
Chromosome Location	chr5:179448057-179448058
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179447316..179449244-chr5:179516942..179519007,2	MCF-7	breast:
2	chr5:179447593..179449240-chr5:179494400..179496143,2	MCF-7	breast:
3	chr5:179439567..179442502-chr5:179447690..179450010,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198995	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10051694	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10056316	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10056991	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10059400	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10066845	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10071652	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10079029	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10464058	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11249663	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11249664	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249665	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11249666	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11739706	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748441	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11750102	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681274	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34585953	0.80[EUR][1000 genomes]
rs3776946	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3776948	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4235505	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4264913	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700852	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700854	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4700859	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57008562	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57117216	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61356660	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62404970	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62404974	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62404976	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62404977	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62404979	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62405015	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6601077	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6601078	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6862105	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6869349	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6873317	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6873639	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6884565	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7729516	0.90[EUR][1000 genomes]
rs7734329	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9329095	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179396600-179461800	Weak transcription	HSMM	muscle
2	chr5:179405200-179453400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:179421800-179462400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:179428600-179462200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:179429400-179452800	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:179429800-179462400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:179429800-179463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:179429800-179463200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:179430000-179453000	Weak transcription	NH-A	brain
11	chr5:179430600-179462400	Weak transcription	HepG2	liver
12	chr5:179434800-179448200	Weak transcription	Fetal Heart	heart
13	chr5:179435200-179448800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:179435400-179453400	Weak transcription	Right Atrium	heart
15	chr5:179435800-179454600	Weak transcription	K562	blood
16	chr5:179436200-179449200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:179436200-179450600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:179437600-179462600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:179438000-179466400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:179439200-179452600	Weak transcription	HUVEC	blood vessel
21	chr5:179439600-179453400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:179440000-179451000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr5:179440000-179453400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:179440200-179457600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:179440200-179462600	Weak transcription	Fetal Intestine Large	intestine
26	chr5:179440600-179462400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:179442600-179448800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:179443400-179452200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:179443800-179451200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:179444000-179452000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:179444200-179453400	Weak transcription	Brain Angular Gyrus	brain
32	chr5:179444600-179448800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr5:179444600-179449200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:179445400-179449200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:179445800-179449800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:179446000-179448800	Weak transcription	Brain Substantia Nigra	brain
37	chr5:179446000-179451800	Weak transcription	Psoas Muscle	Psoas
38	chr5:179446000-179452600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:179446000-179462200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:179446400-179449000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr5:179446400-179449200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr5:179446600-179448800	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:179446600-179450200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:179446600-179450400	Weak transcription	Adipose Nuclei	Adipose
45	chr5:179446800-179448200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr5:179446800-179448200	Strong transcription	Fetal Brain Female	brain
47	chr5:179446800-179448400	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr5:179446800-179448800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr5:179447000-179449000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:179447000-179449800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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