Variant report

Variant	rs2990700
Chromosome Location	chr1:160955726-160955727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12030262	0.81[ASN][1000 genomes]
rs12723902	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12743772	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2243479	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250288	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2481072	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2483143	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483144	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2483148	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28365978	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2988723	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2990701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2990704	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2990705	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3007156	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3007157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656975	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530765	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546890	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9427367	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv10894	chr1:160953742-160960609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv3509633	chr1:160954381-160957557	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2541280	chr1:160954683-160956285	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2990700	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
2	chr1:160948600-160968000	Weak transcription	Ovary	ovary
3	chr1:160952200-160956400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:160952200-160964400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:160952200-160967000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:160952400-160956400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:160952400-160957200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:160953200-160966600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:160953600-160955800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:160953600-160956200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:160953800-160968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:160954000-160956000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:160954000-160956600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:160954200-160959800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:160955400-160956000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr1:160955600-160955800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:160955600-160956000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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