Variant report

Variant	rs9332620
Chromosome Location	chr1:169499951-169499952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169478952..169480932-chr1:169498032..169500995,2	MCF-7	breast:
2	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
3	chr1:169490192..169493609-chr1:169495804..169500257,7	MCF-7	breast:
4	chr1:169475721..169488506-chr1:169493331..169501885,21	MCF-7	breast:
5	chr1:169452411..169456753-chr1:169494976..169501006,10	MCF-7	breast:
6	chr1:169454264..169456422-chr1:169495447..169500944,4	K562	blood:
7	chr1:169454448..169456119-chr1:169499444..169502094,2	K562	blood:

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

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10800450	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800453	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10919178	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919186	0.80[GIH][hapmap]
rs1121789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579441	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12127364	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1557570	0.80[CEU][hapmap];0.92[CHB][hapmap]
rs2009814	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187952	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2213866	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2213867	0.82[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227244	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2239851	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2420373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766103	0.83[CHB][hapmap]
rs3766109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766110	0.85[GIH][hapmap]
rs3820060	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[GIH][hapmap]
rs4524	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4525	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656684	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656685	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]
rs6016	0.81[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6017	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6030	0.93[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs6032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6662696	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6670393	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675244	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6701330	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9287090	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9287092	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9332595	0.85[GIH][hapmap]
rs9332599	0.80[ASN][1000 genomes]
rs9332600	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332627	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332635	0.90[CHB][hapmap];0.84[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332643	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.80[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332651	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332653	0.92[CHB][hapmap]
rs9332655	0.95[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9332665	0.83[CEU][hapmap];0.92[CHB][hapmap]
rs9332667	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs970741	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs974793	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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	nsv872533	chr1:169490401-169508576	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9332620	C1orf112	cis	parietal	SCAN
rs9332620	DCAF6	cis	parietal	SCAN
rs9332620	RXRG	cis	parietal	SCAN
rs9332620	CREG1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169484800-169501000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169485400-169510600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:169487400-169501000	Weak transcription	Right Ventricle	heart
4	chr1:169491600-169500800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:169494000-169502800	Strong transcription	HepG2	liver
6	chr1:169496000-169515200	Strong transcription	Liver	Liver
7	chr1:169496800-169500000	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:169497200-169500000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:169498200-169500000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:169498400-169524000	Weak transcription	Placenta	Placenta
11	chr1:169498600-169500200	Enhancers	HSMMtube	muscle
12	chr1:169498600-169506200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:169498600-169507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:169498800-169501600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr1:169499000-169500000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:169499000-169500000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:169499000-169500000	Weak transcription	HSMM	muscle
18	chr1:169499000-169500200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:169499000-169500200	Enhancers	HMEC	breast
20	chr1:169499000-169500200	Enhancers	NHEK	skin
21	chr1:169499000-169500600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:169499000-169501800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:169499000-169504200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:169499000-169508400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:169499000-169519000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr1:169499200-169500000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:169499200-169500200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:169499200-169500200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:169499600-169500000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:169499800-169500000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:169499800-169500000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:169499800-169500000	Enhancers	K562	blood
33	chr1:169499800-169500200	ZNF genes & repeats	Left Ventricle	heart
34	chr1:169499800-169501800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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