Variant report

Variant	rs2471104
Chromosome Location	chr5:79251504-79251505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:79243051..79245888-chr5:79249775..79252734,2	K562	blood:
2	chr5:79233060..79235575-chr5:79249554..79252283,4	MCF-7	breast:
3	chr5:79249151..79251519-chr5:79253481..79257590,3	K562	blood:
4	chr5:79249486..79252419-chr5:79253972..79256405,2	MCF-7	breast:
5	chr5:79250469..79253672-chr5:79285038..79288543,6	MCF-7	breast:
6	chr5:79251016..79252738-chr5:79254951..79256533,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113296	Chromatin interaction
ENSG00000177034	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10035728	0.80[AFR][1000 genomes]
rs10041212	0.80[AFR][1000 genomes]
rs10041404	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10060444	1.00[JPT][hapmap]
rs10062607	1.00[JPT][hapmap]
rs10065778	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10066471	1.00[JPT][hapmap]
rs10077238	0.84[AFR][1000 genomes]
rs1017996	0.84[AFR][1000 genomes]
rs1017997	0.80[AFR][1000 genomes]
rs1017998	0.80[AFR][1000 genomes]
rs1032341	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1032342	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11741143	0.95[JPT][hapmap]
rs13354864	1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs1370987	1.00[JPT][hapmap]
rs1438739	1.00[JPT][hapmap]
rs16877389	1.00[JPT][hapmap]
rs2291524	0.95[JPT][hapmap]
rs2451929	0.86[AFR][1000 genomes]
rs2451930	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471105	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2471107	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471108	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2471109	0.84[AFR][1000 genomes]
rs6453495	1.00[JPT][hapmap]
rs6453496	1.00[JPT][hapmap]
rs6453497	1.00[JPT][hapmap]
rs6860568	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6865678	0.82[AFR][1000 genomes]
rs6870377	1.00[JPT][hapmap]
rs7446065	0.95[JPT][hapmap];0.80[YRI][hapmap]
rs923634	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]
rs923636	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963423	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs963424	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[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
rs2471104	MTX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79250400-79252600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr5:79250400-79252600	Enhancers	NHDF-Ad	bronchial
3	chr5:79250600-79252600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:79250600-79252600	Enhancers	Fetal Muscle Leg	muscle
5	chr5:79250800-79252000	Enhancers	Fetal Stomach	stomach
6	chr5:79250800-79252400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:79250800-79252600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:79250800-79252600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr5:79250800-79252600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr5:79250800-79252600	Enhancers	HMEC	breast
11	chr5:79250800-79252800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:79250800-79253400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:79250800-79253600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:79251000-79251600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:79251000-79251600	Enhancers	Ovary	ovary
16	chr5:79251000-79252000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr5:79251000-79252000	Enhancers	NHEK	skin
18	chr5:79251000-79252000	Weak transcription	Osteobl	bone
19	chr5:79251000-79252400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:79251000-79252400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:79251000-79254000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:79251200-79251600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr5:79251200-79251600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:79251200-79251600	Weak transcription	HSMMtube	muscle
25	chr5:79251200-79252200	Weak transcription	Esophagus	oesophagus
26	chr5:79251200-79252600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:79251200-79252600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr5:79251200-79252800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:79251200-79252800	Enhancers	HSMM	muscle

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