Variant report

Variant	rs1345085
Chromosome Location	chr5:179512144-179512145
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179496103..179499035-chr5:179510851..179514542,4	K562	blood:
2	chr5:179497319..179499355-chr5:179510354..179513148,3	MCF-7	breast:
3	chr5:179332164..179334090-chr5:179510604..179512176,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10067073	1.00[CEU][hapmap]
rs10072792	0.87[EUR][1000 genomes]
rs10078845	1.00[CEU][hapmap]
rs10479556	1.00[CEU][hapmap]
rs10479558	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479559	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10479560	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10516141	1.00[CEU][hapmap]
rs1110145	0.96[EUR][1000 genomes]
rs11952090	0.96[EUR][1000 genomes]
rs12514260	1.00[CEU][hapmap]
rs12516233	1.00[CEU][hapmap]
rs12516364	1.00[CEU][hapmap]
rs12516629	1.00[CEU][hapmap]
rs12516767	1.00[CEU][hapmap]
rs12521819	0.87[EUR][1000 genomes]
rs13354862	1.00[CEU][hapmap]
rs13362131	1.00[CEU][hapmap]
rs1345087	1.00[EUR][1000 genomes]
rs1345088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17079941	1.00[CEU][hapmap]
rs1808088	1.00[CEU][hapmap]
rs2009732	0.95[AFR][1000 genomes]
rs28478989	0.87[EUR][1000 genomes]
rs4623110	1.00[CEU][hapmap]
rs58286692	0.83[EUR][1000 genomes]
rs59668758	0.87[EUR][1000 genomes]
rs9654545	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179499400-179517000	Weak transcription	Right Atrium	heart
2	chr5:179508000-179513000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:179508400-179513000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:179508600-179513800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:179508800-179514200	Enhancers	H1 Cell Line	embryonic stem cell
6	chr5:179509000-179513200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:179509000-179513200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179509200-179512400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:179509200-179512600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:179509200-179514400	Enhancers	H9 Cell Line	embryonic stem cell
11	chr5:179509400-179517200	Weak transcription	Liver	Liver
12	chr5:179509600-179513400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:179509800-179512800	Enhancers	Brain Germinal Matrix	brain
14	chr5:179510200-179513200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr5:179510200-179513800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:179510400-179512800	Weak transcription	Fetal Brain Male	brain
17	chr5:179510600-179513200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr5:179510600-179517000	Weak transcription	Fetal Brain Female	brain
19	chr5:179510800-179512200	Weak transcription	Brain Anterior Caudate	brain
20	chr5:179510800-179512600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr5:179510800-179512600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr5:179511000-179512200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:179511000-179514400	Enhancers	Primary hematopoietic stem cells	blood
24	chr5:179511200-179512200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:179511200-179512800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr5:179511200-179512800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr5:179511200-179513000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:179511200-179513200	Enhancers	Pancreas	Pancrea
29	chr5:179511200-179514000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr5:179511400-179512200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr5:179511600-179512200	Enhancers	Fetal Intestine Small	intestine
32	chr5:179511600-179512400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:179511600-179512400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:179511600-179512600	Enhancers	Placenta	Placenta
35	chr5:179511600-179513000	Enhancers	Duodenum Mucosa	Duodenum
36	chr5:179511600-179513000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr5:179511800-179512200	Enhancers	Lung	lung
38	chr5:179511800-179512400	Weak transcription	Spleen	Spleen
39	chr5:179511800-179512400	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr5:179511800-179512600	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr5:179511800-179513000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:179511800-179513000	Enhancers	Fetal Intestine Large	intestine
43	chr5:179511800-179513000	Enhancers	Stomach Mucosa	stomach
44	chr5:179511800-179513200	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr5:179511800-179514200	Enhancers	Fetal Thymus	thymus
46	chr5:179512000-179512200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr5:179512000-179512600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr5:179512000-179512600	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr5:179512000-179512600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:179512000-179512600	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links