Variant report

Variant	rs6671490
Chromosome Location	chr1:160852700-160852701
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160850691..160852389-chr1:160852476..160855044,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179914	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10797087	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908808	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908809	0.85[EUR][1000 genomes]
rs10908810	0.82[EUR][1000 genomes]
rs10908811	0.82[EUR][1000 genomes]
rs10908812	0.82[EUR][1000 genomes]
rs11265510	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11265514	0.82[EUR][1000 genomes]
rs11265516	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11265519	0.82[EUR][1000 genomes]
rs11578752	0.84[EUR][1000 genomes]
rs12135639	0.81[EUR][1000 genomes]
rs12409609	0.91[EUR][1000 genomes]
rs12566557	0.80[AMR][1000 genomes]
rs1333062	0.91[EUR][1000 genomes]
rs17387157	0.92[EUR][1000 genomes]
rs1810924	0.82[EUR][1000 genomes]
rs1855187	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1930596	0.82[EUR][1000 genomes]
rs2039415	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2225591	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236515	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2274905	0.92[EUR][1000 genomes]
rs2274907	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274908	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274909	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2274910	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2297559	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34067571	0.87[EUR][1000 genomes]
rs3766356	0.92[EUR][1000 genomes]
rs3766357	0.92[EUR][1000 genomes]
rs3766359	0.92[EUR][1000 genomes]
rs3818724	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3820094	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656951	0.86[EUR][1000 genomes]
rs4656953	0.91[EUR][1000 genomes]
rs4656955	0.92[EUR][1000 genomes]
rs4656956	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656957	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4656958	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656959	0.84[EUR][1000 genomes]
rs6427550	0.92[EUR][1000 genomes]
rs6427551	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6427552	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6427553	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6658416	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6667400	0.87[EUR][1000 genomes]
rs6691868	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6694415	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6703406	0.92[EUR][1000 genomes]
rs6704490	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7411035	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7414826	0.84[EUR][1000 genomes]
rs7524351	0.92[EUR][1000 genomes]
rs7532133	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7551697	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs869167	0.83[AMR][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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	esv3430322	chr1:160851829-160920480	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6671490	RP11-312J18.6	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160846800-160854200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:160847600-160853800	Weak transcription	Spleen	Spleen
3	chr1:160849200-160855400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:160849400-160854200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160851000-160855400	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:160851200-160852800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:160852400-160855000	Enhancers	Primary neutrophils fromperipheralblood	blood

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