Variant report

Variant	rs1828930
Chromosome Location	chr2:11291036-11291037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:11290827-11291237	MCF-7	breast:	n/a	n/a
2	GATA3	chr2:11290660-11291445	MCF-7	breast:	n/a	n/a
3	GATA3	chr2:11290650-11291598	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:11290663-11291358	T-47D	breast:	n/a	n/a
5	NR2F2	chr2:11290751-11291397	MCF-7	breast:	n/a	n/a
6	GATA3	chr2:11290678-11291274	T-47D	breast:	n/a	n/a
7	GATA2	chr2:11290806-11291171	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr2:11290866-11291150	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11289895..11292620-chr2:11293697..11297329,4	MCF-7	breast:
2	chr2:11289560..11291933-chr2:11293311..11295693,2	K562	blood:

Variant related genes	Relation type
PQLC3	TF binding region
ENSG00000162976	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10929723	0.88[ASN][1000 genomes]
rs10929724	0.86[ASN][1000 genomes]
rs11676692	1.00[ASN][1000 genomes]
rs11683786	0.86[CHB][hapmap]
rs11892387	0.88[AMR][1000 genomes]
rs12470798	0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12612929	0.88[ASN][1000 genomes]
rs12615623	0.85[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs12987119	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12994920	0.87[ASN][1000 genomes]
rs12995564	0.89[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs13000987	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13022766	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13027444	0.88[AMR][1000 genomes]
rs13028675	0.86[ASN][1000 genomes]
rs13030385	0.86[ASN][1000 genomes]
rs13031027	0.86[ASN][1000 genomes]
rs17366322	0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs34315339	0.86[ASN][1000 genomes]
rs34333866	0.88[ASN][1000 genomes]
rs34344767	0.88[ASN][1000 genomes]
rs36026430	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668716	0.80[ASN][1000 genomes]
rs4669695	0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs55975936	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744659	0.88[ASN][1000 genomes]
rs6754718	0.88[ASN][1000 genomes]
rs6754745	0.88[ASN][1000 genomes]
rs71439048	0.88[ASN][1000 genomes]
rs727803	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581322	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7586305	0.83[ASN][1000 genomes]
rs7601782	0.81[ASN][1000 genomes]
rs7606827	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1828930	PQLC3	cis	Esophagus Mucosa	GTEx
rs1828930	PQLC3	cis	Thyroid	GTEx
rs1828930	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs1828930	PQLC3	cis	lung	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11273600-11294400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:11274000-11294600	Weak transcription	Right Atrium	heart
3	chr2:11284600-11294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:11288000-11292000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:11288000-11294200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr2:11288200-11294400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr2:11288200-11294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:11289600-11294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:11289800-11294400	Weak transcription	Pancreas	Pancrea
10	chr2:11291000-11291400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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