Variant report

Variant	rs6027
Chromosome Location	chr1:169483561-169483562
allele	A/G
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
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10800452	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919147	1.00[ASW][hapmap]
rs10919158	1.00[ASW][hapmap]
rs10919184	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919185	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12024849	0.95[ASN][1000 genomes]
rs12025910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239964	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405595	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557571	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17345426	1.00[ASW][hapmap]
rs17518147	1.00[ASW][hapmap]
rs1800595	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1894691	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs1894693	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1894703	1.00[ASW][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs2227243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301516	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301519	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2301520	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2420134	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420135	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766104	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440913	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[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]
rs6015	0.87[CHD][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs6018	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6024	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6033	1.00[MKK][hapmap];1.00[TSI][hapmap]
rs6036	0.87[CHD][hapmap];1.00[TSI][hapmap]
rs6037	0.87[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs72708008	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708039	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7556463	1.00[ASW][hapmap]
rs916439	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332601	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332609	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332614	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9332629	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9332639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332646	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332654	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[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]
rs9332673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332676	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966751	1.00[AFR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6027	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 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	chr1:169480600-169483600	Weak transcription	HepG2	liver
6	chr1:169480800-169483800	Weak transcription	HSMMtube	muscle
7	chr1:169481000-169484000	Weak transcription	Stomach Mucosa	stomach
8	chr1:169481200-169484000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:169481400-169483600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:169481400-169485000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:169481800-169483600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:169481800-169483800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:169481800-169493000	Strong transcription	Liver	Liver
14	chr1:169482000-169483600	Enhancers	Adipose Nuclei	Adipose
15	chr1:169482000-169484800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:169482600-169483600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:169482600-169483800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:169482600-169490800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:169482800-169487600	Weak transcription	Ovary	ovary
20	chr1:169483000-169483800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:169483000-169484000	Weak transcription	HMEC	breast
22	chr1:169483000-169484200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:169483000-169484400	Weak transcription	Placenta	Placenta
24	chr1:169483200-169483600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:169483200-169483600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:169483200-169483600	Weak transcription	NHEK	skin
27	chr1:169483200-169483800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:169483200-169495400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:169483200-169496800	Strong transcription	Monocytes-CD14+_RO01746	blood

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