Variant report

Variant	rs11119758
Chromosome Location	chr1:211694198-211694199
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211686791..211692090-chr1:211692436..211697358,7	K562	blood:
2	chr1:211692734..211695713-chr1:211744143..211747035,2	MCF-7	breast:
3	chr1:211694132..211696485-chr1:211743577..211746464,2	MCF-7	breast:
4	chr1:211687723..211692261-chr1:211692405..211697712,7	MCF-7	breast:
5	chr1:211688371..211691980-chr1:211692436..211695699,4	K562	blood:
6	chr1:211693758..211694545-chr1:211798120..211798669,2	MCF-7	breast:
7	chr1:211693675..211694499-chr1:211828424..211829182,3	MCF-7	breast:
8	chr1:211692018..211701005-chr1:211746984..211755135,17	MCF-7	breast:
9	chr1:211692714..211696685-chr1:211696869..211699786,3	K562	blood:

No data

No data

No data

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10863915	0.89[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962917	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1962918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2010504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951528	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4951758	0.88[JPT][hapmap];0.96[LWK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs4951762	1.00[CHB][hapmap];1.00[JPT][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]
rs6664769	0.83[AMR][1000 genomes]
rs6680424	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7519203	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	nsv832514	chr1:211630247-211794963	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv1826724	chr1:211684336-211694508	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11119758	LGTN	cis	parietal	SCAN
rs11119758	IL10	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211688200-211701200	Weak transcription	Gastric	stomach
2	chr1:211689400-211694400	Weak transcription	Right Atrium	heart
3	chr1:211689400-211701200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:211689400-211715000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:211690200-211698400	Enhancers	Liver	Liver
6	chr1:211690400-211695800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:211690800-211694400	Weak transcription	K562	blood
8	chr1:211690800-211694600	Weak transcription	A549	lung
9	chr1:211691000-211700400	Weak transcription	Fetal Thymus	thymus
10	chr1:211691200-211694400	Weak transcription	Hela-S3	cervix
11	chr1:211692400-211694200	Enhancers	GM12878-XiMat	blood
12	chr1:211693400-211697800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:211693800-211695000	Flanking Active TSS	HepG2	liver

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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