Variant report

Variant	rs2239852
Chromosome Location	chr1:169512524-169512525
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	chr1:169449555..169458933-chr1:169508181..169519645,22	MCF-7	breast:
2	chr1:169453402..169457978-chr1:169510259..169517954,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1046712	0.98[ASN][1000 genomes]
rs10800454	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800456	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1557570	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs1557572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1894694	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2157581	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298909	0.87[CEU][hapmap]
rs2301515	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3820060	0.96[CEU][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4656185	0.82[EUR][1000 genomes]
rs4656687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6021	0.82[CEU][hapmap]
rs6030	0.96[CEU][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs61805767	0.92[ASN][1000 genomes]
rs6686805	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701330	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7535409	0.86[EUR][1000 genomes]
rs916438	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9332599	0.84[EUR][1000 genomes]
rs9332627	0.83[CEU][hapmap]
rs9332655	0.91[CEU][hapmap]
rs9332665	0.95[CEU][hapmap];0.82[EUR][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2239852	C1orf112	cis	parietal	SCAN
rs2239852	XCL2	cis	cerebellum	SCAN
rs2239852	DCAF6	cis	parietal	SCAN
rs2239852	C1orf129	cis	cerebellum	SCAN
rs2239852	SELL	cis	cerebellum	SCAN
rs2239852	RXRG	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169496000-169515200	Strong transcription	Liver	Liver
2	chr1:169498400-169524000	Weak transcription	Placenta	Placenta
3	chr1:169499000-169519000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:169500200-169526800	Weak transcription	Left Ventricle	heart
5	chr1:169504000-169515000	Strong transcription	HepG2	liver
6	chr1:169505800-169534800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:169506200-169542800	Weak transcription	Right Ventricle	heart
8	chr1:169507000-169530800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:169508800-169513200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:169509600-169515600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:169510200-169515800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:169510600-169513600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:169510800-169513400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:169510800-169515600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:169511000-169520000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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