Variant report

Variant	rs405878
Chromosome Location	chr5:79296906-79296907
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	chr5:79220441..79221400-chr5:79296482..79297375,4	MCF-7	breast:
2	chr5:79220191..79221034-chr5:79296621..79297178,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THBS4-4	chr5:79294156-79304207	NONHSAT102380

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10035728	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10041212	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10041404	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10043116	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10060444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10062607	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10064975	0.95[CEU][hapmap]
rs10065778	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10066471	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10071601	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077238	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1017996	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1017997	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1017998	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1032342	0.91[JPT][hapmap]
rs11741143	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11748289	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13354864	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1370987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1438739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16877389	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404708	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2451929	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2451930	0.82[EUR][1000 genomes]
rs2471104	0.95[JPT][hapmap]
rs2471105	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs2471107	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2471108	0.82[EUR][1000 genomes]
rs2471109	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs422690	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6453494	0.93[EUR][1000 genomes]
rs6453495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6453496	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6453497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6860568	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6865678	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6868916	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6870377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6873684	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6882768	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6887873	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6892826	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7446065	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7707036	0.87[ASN][1000 genomes]
rs7734858	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923634	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs923636	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs9293795	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963423	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs963424	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs405878	MTX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79287600-79311400	Weak transcription	Aorta	Aorta
2	chr5:79287800-79299800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:79288000-79297200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:79288000-79297400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:79288000-79297600	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:79288000-79298000	Weak transcription	HSMM	muscle
7	chr5:79288000-79299000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:79288000-79303200	Weak transcription	Pancreas	Pancrea
9	chr5:79288000-79311000	Weak transcription	Ovary	ovary
10	chr5:79288200-79297200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:79288200-79310400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:79288200-79311800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:79288800-79297000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:79292000-79315600	Weak transcription	HSMMtube	muscle
15	chr5:79294200-79298000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:79294800-79298200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:79296000-79302000	Weak transcription	NHEK	skin
18	chr5:79296400-79297400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:79296400-79299200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:79296800-79306400	Weak transcription	Psoas Muscle	Psoas

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