Variant report

Variant	rs4656685
Chromosome Location	chr1:169483844-169483845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169475240..169477243-chr1:169482171..169484444,2	MCF-7	breast:
2	chr1:169481648..169484694-chr1:169484880..169487777,3	MCF-7	breast:
3	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
4	chr1:169454713..169456671-chr1:169482911..169484828,2	K562	blood:
5	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
6	chr1:169482503..169484196-chr1:169484745..169487680,2	K562	blood:
7	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: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10800450	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800453	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10919178	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1121789	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579441	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127364	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1557570	0.80[CEU][hapmap];0.84[CHB][hapmap]
rs2009814	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187952	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]
rs2187953	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2213866	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2213867	0.82[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239851	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766103	0.92[CHB][hapmap]
rs3766109	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766110	0.83[GIH][hapmap]
rs3820060	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]
rs4524	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4525	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656185	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4656187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656684	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6016	0.95[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6017	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6021	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6030	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.81[MKK][hapmap]
rs6032	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662593	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662696	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670393	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675244	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6701330	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs9287090	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9287092	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9332595	0.83[GIH][hapmap]
rs9332600	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9332619	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332620	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332627	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332635	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332643	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332651	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332653	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9332655	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332665	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9332667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970741	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4656685	RXRG	cis	parietal	SCAN
rs4656685	CREG1	cis	parietal	SCAN
rs4656685	GPR161	cis	parietal	SCAN
rs4656685	XCL2	cis	cerebellum	SCAN
rs4656685	C1orf112	cis	parietal	SCAN
rs4656685	DCAF6	cis	parietal	SCAN

Chromatin state (count:26 , 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	chr1:169478800-169484000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:169478800-169488200	Weak transcription	Small Intestine	intestine
4	chr1:169479400-169485000	Enhancers	Hela-S3	cervix
5	chr1:169481000-169484000	Weak transcription	Stomach Mucosa	stomach
6	chr1:169481200-169484000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:169481400-169485000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:169481800-169493000	Strong transcription	Liver	Liver
9	chr1:169482000-169484800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:169482600-169490800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:169482800-169487600	Weak transcription	Ovary	ovary
12	chr1:169483000-169484000	Weak transcription	HMEC	breast
13	chr1:169483000-169484200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:169483000-169484400	Weak transcription	Placenta	Placenta
15	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:169483600-169484000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:169483600-169484200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:169483600-169484200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:169483600-169484200	Enhancers	NHEK	skin
21	chr1:169483600-169484800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:169483600-169486000	Strong transcription	HepG2	liver
23	chr1:169483800-169484200	Enhancers	HSMMtube	muscle
24	chr1:169483800-169484800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:169483800-169486000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:169483800-169496800	Strong transcription	Primary monocytes fromperipheralblood	blood

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