Variant report

Variant	rs923634
Chromosome Location	chr5:79253031-79253032
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	chr5:79252333..79253868-chr5:79285797..79288103,2	MCF-7	breast:
2	chr5:79250469..79253672-chr5:79285038..79288543,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177034	Chromatin interaction
ENSG00000113296	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10035728	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10041212	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10041404	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10043116	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10060444	0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10062607	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs10065778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10066471	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10071601	0.81[EUR][1000 genomes]
rs10077238	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1017996	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1017997	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1017998	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1032341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1032342	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741143	0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs11748289	0.80[AMR][1000 genomes]
rs13354864	0.95[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1370987	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs1438739	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs16877389	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2291524	0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2404708	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2451929	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2451930	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2471104	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2471106	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2471107	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2471108	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2471109	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs405878	0.80[EUR][1000 genomes]
rs422690	0.80[EUR][1000 genomes]
rs6453495	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6453496	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6453497	0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs6860568	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6865678	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6868916	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6870377	0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs6873684	0.80[EUR][1000 genomes]
rs6882768	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6887873	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6892826	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7446065	0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7734858	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923636	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9293795	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs963423	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs963424	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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
2	esv1822393	chr5:79195538-79260489	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs923634	MTX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79250800-79253400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:79250800-79253600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:79251000-79254000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:79251600-79253200	Enhancers	HSMMtube	muscle
5	chr5:79251600-79253400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:79251800-79257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:79252400-79257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:79252600-79256800	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:79252600-79257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:79252600-79258200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:79252800-79253600	Enhancers	HMEC	breast
12	chr5:79252800-79253600	Enhancers	NHEK	skin
13	chr5:79252800-79258000	Weak transcription	NH-A	brain
14	chr5:79252800-79258200	Weak transcription	HSMM	muscle

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