Variant report

Variant	rs3820060
Chromosome Location	chr1:169484552-169484553
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169481648..169484694-chr1:169484880..169487777,3	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169454713..169456671-chr1:169482911..169484828,2	K562	blood:
4	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
5	chr1:169483273..169484944-chr1:169493711..169496257,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10800450	0.83[ASN][1000 genomes]
rs10800454	0.83[EUR][1000 genomes]
rs10800456	0.83[CEU][hapmap]
rs10919178	0.81[ASN][1000 genomes]
rs1121789	0.82[CEU][hapmap];0.90[CHB][hapmap]
rs11579441	0.81[ASN][1000 genomes]
rs1557570	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1557572	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2009814	0.82[ASN][1000 genomes]
rs2040444	0.94[JPT][hapmap]
rs2157581	0.85[EUR][1000 genomes]
rs2187952	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs2213866	0.81[ASN][1000 genomes]
rs2213867	0.81[ASN][1000 genomes]
rs2227244	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2239851	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs2239852	0.96[CEU][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2298909	0.82[CEU][hapmap]
rs2301515	0.96[CEU][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs2420369	0.94[JPT][hapmap]
rs3766103	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs3766109	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs4524	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs4525	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs4656185	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656187	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs4656684	0.82[ASN][1000 genomes]
rs4656685	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.80[MKK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4656687	0.96[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6016	0.81[GIH][hapmap]
rs6017	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs6021	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs6030	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6032	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs6662593	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs6670407	0.94[JPT][hapmap]
rs6686805	0.82[EUR][1000 genomes]
rs6701330	1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535409	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs916438	0.96[CEU][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs9332599	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9332600	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs9332619	0.83[CEU][hapmap];0.92[CHB][hapmap];0.83[GIH][hapmap]
rs9332620	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs9332627	0.87[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs9332635	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9332643	0.83[CEU][hapmap];0.92[CHB][hapmap];0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs9332653	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9332655	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9332665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332667	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs970741	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs974793	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.89[YRI][hapmap];0.82[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	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
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3820060	XCL2	cis	cerebellum	SCAN
rs3820060	C1orf129	cis	cerebellum	SCAN
rs3820060	RXRG	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169478200-169487000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr1:169478800-169488200	Weak transcription	Small Intestine	intestine
3	chr1:169479400-169485000	Enhancers	Hela-S3	cervix
4	chr1:169481400-169485000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:169481800-169493000	Strong transcription	Liver	Liver
6	chr1:169482000-169484800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:169482600-169490800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:169482800-169487600	Weak transcription	Ovary	ovary
9	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:169483600-169484800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:169483600-169486000	Strong transcription	HepG2	liver
13	chr1:169483800-169484800	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:169483800-169486000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:169483800-169496800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:169484000-169484600	Enhancers	Stomach Mucosa	stomach
17	chr1:169484000-169484800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:169484000-169484800	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr1:169484200-169484800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr1:169484200-169487600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr1:169484200-169494400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:169484400-169485000	Strong transcription	Placenta	Placenta

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