Variant report

Variant	rs2404708
Chromosome Location	chr5:79272431-79272432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79249284..79251451-chr5:79270809..79273026,3	MCF-7	breast:
2	chr5:79269309..79272565-chr5:79276555..79279232,3	MCF-7	breast:
3	chr5:79262485..79266204-chr5:79269459..79273570,3	MCF-7	breast:
4	chr5:79271074..79273933-chr5:79292218..79294924,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10035728	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10041212	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10041404	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10043116	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10060444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10062607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10064975	0.95[CEU][hapmap]
rs10065778	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10066471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10071601	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10077238	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1017996	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1017997	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1017998	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1032341	0.84[AMR][1000 genomes]
rs1032342	0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs11741143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11748289	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13354864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1438739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16877389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2451929	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2451930	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2471104	1.00[JPT][hapmap]
rs2471105	0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2471107	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2471108	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2471109	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs405878	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs422690	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6453494	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6453495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6453496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6453497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6860568	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6865678	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6868916	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6870377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6873684	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6882768	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6887873	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6889652	0.86[AFR][1000 genomes]
rs6892826	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7446065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7707036	0.82[ASN][1000 genomes]
rs7734858	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs923634	0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs923636	0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9293795	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs963423	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs963424	0.85[AMR][1000 genomes];0.82[EUR][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	nsv1021113	chr5:79034662-79289828	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2404708	MTX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79259400-79272800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:79260600-79286200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:79263200-79273200	Weak transcription	Psoas Muscle	Psoas
4	chr5:79267400-79272600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:79267400-79272800	Weak transcription	Fetal Brain Female	brain
6	chr5:79267600-79272600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:79267600-79273000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:79267800-79273600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr5:79268000-79273000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:79268000-79273000	Weak transcription	Fetal Intestine Large	intestine
11	chr5:79268000-79273800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:79268200-79273000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:79268200-79273000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr5:79268200-79273000	Weak transcription	GM12878-XiMat	blood
15	chr5:79268400-79273600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr5:79268600-79273000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:79269000-79272800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:79269000-79273000	Weak transcription	Aorta	Aorta
19	chr5:79269000-79273000	Weak transcription	Fetal Lung	lung
20	chr5:79269000-79286400	Weak transcription	Thymus	Thymus
21	chr5:79269200-79274800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:79269400-79272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:79269400-79273000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr5:79269400-79277800	Weak transcription	Hela-S3	cervix
25	chr5:79269400-79279200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:79269600-79272800	Weak transcription	Brain Angular Gyrus	brain
27	chr5:79269600-79273200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:79269600-79273200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr5:79269600-79273800	Weak transcription	Colonic Mucosa	Colon
30	chr5:79269600-79276000	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:79269600-79276600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:79269600-79277800	Weak transcription	Brain Anterior Caudate	brain
33	chr5:79269800-79272600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:79269800-79272800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:79269800-79272800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:79269800-79273600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr5:79269800-79273600	Weak transcription	Brain Germinal Matrix	brain
38	chr5:79269800-79279200	Weak transcription	Brain Substantia Nigra	brain
39	chr5:79269800-79279400	Weak transcription	Lung	lung
40	chr5:79269800-79281400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:79269800-79286000	Weak transcription	Fetal Heart	heart
42	chr5:79270000-79272800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:79270000-79273000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:79270000-79273000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:79270000-79273800	Weak transcription	Esophagus	oesophagus
46	chr5:79270000-79276400	Strong transcription	Primary B cells from cord blood	blood
47	chr5:79270000-79276400	Weak transcription	Fetal Kidney	kidney
48	chr5:79270000-79286000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr5:79270200-79276000	Weak transcription	Colon Smooth Muscle	Colon
50	chr5:79270200-79286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links