Variant report

Variant	rs2434279
Chromosome Location	chr5:79388459-79388460
allele	C/T
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:
2	chr5:79387676..79388570-chr5:79603076..79603754,4	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2434287	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2438642	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2438644	0.81[ASN][1000 genomes]
rs7727310	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2434279	MTX3	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:79386800-79388600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:79387200-79389200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:79387400-79389400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr5:79387400-79389400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:79387400-79389600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:79387400-79389800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:79387400-79389800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:79387400-79389800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr5:79387400-79397000	Enhancers	Fetal Thymus	thymus
19	chr5:79387600-79388800	Enhancers	Dnd41	blood
20	chr5:79387600-79388800	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr5:79387600-79389000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:79387600-79389600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr5:79387600-79389800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:79387800-79388800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:79387800-79389000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr5:79387800-79389000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:79387800-79389200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:79387800-79389200	Weak transcription	Fetal Kidney	kidney
29	chr5:79388000-79388600	Enhancers	Primary hematopoietic stem cells	blood
30	chr5:79388000-79388800	Enhancers	Thymus	Thymus
31	chr5:79388000-79389800	Enhancers	Primary T cells from cord blood	blood
32	chr5:79388000-79405000	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:79388200-79389000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:79388200-79389400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr5:79388200-79389400	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:79388200-79389800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:79388400-79388600	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr5:79388400-79388800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr5:79388400-79389400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:79388400-79389600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:79388400-79389600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr5:79388400-79389600	Weak transcription	Pancreas	Pancrea
43	chr5:79388400-79390000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr5:79388400-79390400	Weak transcription	Right Atrium	heart
45	chr5:79388400-79393400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links