Variant report

Variant	rs2434280
Chromosome Location	chr5:79388765-79388766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79387918..79390143-chr5:79603120..79605214,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10474605	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1438735	0.82[EUR][1000 genomes]
rs1438737	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs166270	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2059794	0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs2241825	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249687	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2249794	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2434277	0.82[CEU][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2434278	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2434282	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2434299	0.83[EUR][1000 genomes]
rs2434301	0.83[EUR][1000 genomes]
rs2434302	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2434303	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2434304	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2438641	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2438644	0.92[EUR][1000 genomes]
rs2438645	0.84[EUR][1000 genomes]
rs2438649	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs256442	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs256445	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2913544	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2918422	0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs364988	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs368287	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs368936	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs380747	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs382746	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs384941	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs394947	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs397601	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs404375	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs405112	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs407314	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs411240	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs411943	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs412379	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs426623	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs428279	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs432267	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6861685	0.80[ASN][1000 genomes]
rs689879	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs690284	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs690325	0.81[EUR][1000 genomes]
rs692979	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs693270	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv598744	chr5:79388745-79423347	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79366200-79392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:79379400-79393200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr5:79379400-79400600	Weak transcription	Left Ventricle	heart
4	chr5:79382000-79393200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:79385000-79389400	Enhancers	HepG2	liver
6	chr5:79385200-79389400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:79385400-79389000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:79385400-79389200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:79385800-79393000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:79387200-79389200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:79387400-79389400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr5:79387400-79389400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:79387400-79389600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:79387400-79389800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:79387400-79389800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:79387400-79389800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:79387400-79397000	Enhancers	Fetal Thymus	thymus
18	chr5:79387600-79388800	Enhancers	Dnd41	blood
19	chr5:79387600-79388800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr5:79387600-79389000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr5:79387600-79389600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr5:79387600-79389800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:79387800-79388800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:79387800-79389000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr5:79387800-79389000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:79387800-79389200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:79387800-79389200	Weak transcription	Fetal Kidney	kidney
28	chr5:79388000-79388800	Enhancers	Thymus	Thymus
29	chr5:79388000-79389800	Enhancers	Primary T cells from cord blood	blood
30	chr5:79388000-79405000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr5:79388200-79389000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:79388200-79389400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr5:79388200-79389400	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:79388200-79389800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:79388400-79388800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr5:79388400-79389400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:79388400-79389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:79388400-79389600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:79388400-79389600	Weak transcription	Pancreas	Pancrea
40	chr5:79388400-79390000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr5:79388400-79390400	Weak transcription	Right Atrium	heart
42	chr5:79388400-79393400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:79388600-79389400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:79388600-79390400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:79388600-79395600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links