Variant report

Variant	rs10489364
Chromosome Location	chr1:168867600-168867601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168865232..168870287-chr1:169075405..169077247,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP1B1-3	chr1:168867374-168867677	NONHSAT007449

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1022789	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1028642	0.85[JPT][hapmap]
rs10753781	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800392	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800393	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800395	0.84[ASN][1000 genomes]
rs10919011	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919013	0.90[JPT][hapmap]
rs1570335	1.00[ASW][hapmap];0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2065128	0.82[CEU][hapmap]
rs2065129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2146205	0.86[JPT][hapmap]
rs4142003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656163	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4656166	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4656622	0.82[EUR][1000 genomes]
rs4656624	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6427155	0.82[EUR][1000 genomes]
rs6427157	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427159	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6657987	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670083	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6670091	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683127	0.81[EUR][1000 genomes]
rs6683236	0.80[EUR][1000 genomes]
rs6683991	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[TSI][hapmap]
rs7514435	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7527859	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7550083	0.80[EUR][1000 genomes]
rs7551577	0.84[CEU][hapmap]

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	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv437258	chr1:168824111-168890420	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10489364	MAEL	cis	parietal	SCAN
rs10489364	XCL1	cis	parietal	SCAN
rs10489364	POGK	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168862400-168877000	Weak transcription	Fetal Heart	heart
2	chr1:168863200-168867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:168863200-168867800	Weak transcription	NHEK	skin
4	chr1:168863200-168868000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:168863200-168868400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:168867000-168875600	Weak transcription	Placenta Amnion	Placenta Amnion

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