Variant report

Variant	rs164860
Chromosome Location	chr5:14268943-14268944
allele	A/C
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:14155881..14158811-chr5:14267142..14271683,5	MCF-7	breast:
2	chr5:14268388..14270560-chr5:14279679..14282134,3	MCF-7	breast:
3	chr5:14036740..14039261-chr5:14266762..14269658,3	MCF-7	breast:
4	chr5:14267248..14270111-chr5:14276512..14278649,2	K562	blood:
5	chr5:14268455..14270737-chr5:14277018..14279367,2	MCF-7	breast:
6	chr5:14264035..14266359-chr5:14267149..14269027,3	MCF-7	breast:
7	chr5:14142083..14147002-chr5:14262644..14273159,29	MCF-7	breast:
8	chr5:14262017..14264062-chr5:14267525..14269616,2	K562	blood:
9	chr5:14141187..14146160-chr5:14268118..14270576,7	MCF-7	breast:
10	chr5:14034068..14036123-chr5:14267082..14269872,2	MCF-7	breast:
11	chr5:14036353..14038493-chr5:14267240..14270155,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12522960	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs154150	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs164859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs164862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs164863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs165092	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs165094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs165095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs165096	0.89[ASN][1000 genomes]
rs16903338	0.90[JPT][hapmap]
rs2440982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30618	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs30621	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs30626	0.90[ASN][1000 genomes]
rs30627	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30629	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs30630	0.91[ASN][1000 genomes]
rs30631	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs30632	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs30633	0.82[CHB][hapmap]
rs30635	0.82[ASN][1000 genomes]
rs354303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs356026	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356027	0.91[ASN][1000 genomes]
rs356028	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356029	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs42253	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4701604	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56334634	0.89[ASN][1000 genomes]
rs58221971	0.87[ASN][1000 genomes]
rs6554849	0.87[ASN][1000 genomes]
rs6554850	0.89[ASN][1000 genomes]
rs6554851	0.89[ASN][1000 genomes]
rs7380307	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs7700787	0.82[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14262200-14270800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:14265200-14271400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:14265200-14293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:14265400-14269000	Weak transcription	Liver	Liver
5	chr5:14265400-14269200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:14265400-14269400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr5:14265400-14269400	Weak transcription	Fetal Intestine Small	intestine
8	chr5:14265400-14269400	Weak transcription	Fetal Lung	lung
9	chr5:14265400-14269600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:14265400-14270400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:14265400-14270600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr5:14265400-14270800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr5:14265400-14270800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:14265400-14270800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:14265400-14270800	Enhancers	Fetal Brain Male	brain
16	chr5:14265400-14271000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:14265400-14271200	Enhancers	NHLF	lung
18	chr5:14265400-14272200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:14265400-14277200	Weak transcription	Thymus	Thymus
20	chr5:14265400-14284600	Weak transcription	Stomach Mucosa	stomach
21	chr5:14265400-14286600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:14265600-14270000	Weak transcription	Primary B cells from cord blood	blood
23	chr5:14265600-14270800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:14266000-14270000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr5:14266000-14270400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr5:14266000-14270800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr5:14266400-14269800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr5:14266400-14270600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:14266800-14270000	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr5:14267000-14270400	Enhancers	Fetal Thymus	thymus
31	chr5:14267000-14271000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr5:14267000-14272600	Enhancers	HepG2	liver
33	chr5:14267400-14270400	Enhancers	Ovary	ovary
34	chr5:14267400-14270400	Flanking Active TSS	A549	lung
35	chr5:14267400-14270800	Enhancers	Fetal Muscle Leg	muscle
36	chr5:14267600-14269400	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr5:14267600-14269600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:14267600-14269800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:14267800-14269400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr5:14268000-14269600	Flanking Active TSS	NH-A	brain
41	chr5:14268000-14270400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:14268000-14270400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:14268000-14270400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr5:14268000-14271000	Enhancers	Colon Smooth Muscle	Colon
45	chr5:14268200-14269000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr5:14268200-14269000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:14268200-14269000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:14268200-14269000	Flanking Active TSS	NHDF-Ad	bronchial
49	chr5:14268200-14269200	Flanking Active TSS	Osteobl	bone
50	chr5:14268200-14269600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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