Variant report

Variant	rs11119971
Chromosome Location	chr1:212729811-212729812
allele	A/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
2	chr1:212457639..212459855-chr1:212727032..212729860,2	K562	blood:
3	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
4	chr1:212651265..212654246-chr1:212726991..212729981,2	K562	blood:
5	chr1:212729371..212731650-chr1:212796450..212799442,2	K562	blood:
6	chr1:212728800..212730367-chr1:212781443..212783731,2	MCF-7	breast:
7	chr1:212713256..212715343-chr1:212729431..212731008,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264590	Chromatin interaction
ENSG00000066027	Chromatin interaction
ENSG00000162771	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10779581	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10863978	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10863979	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863980	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10863981	0.86[JPT][hapmap]
rs11119940	1.00[ASW][hapmap]
rs11119941	1.00[ASW][hapmap]
rs11119956	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11119957	0.95[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11119962	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11119963	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11119965	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119972	0.95[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11119973	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11119974	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11119975	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11119977	0.85[JPT][hapmap]
rs12038766	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs12041940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136405	0.85[AMR][1000 genomes]
rs12729140	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs3806460	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs4951447	1.00[ASW][hapmap]
rs4951448	1.00[ASW][hapmap]
rs4951453	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951606	0.90[CHB][hapmap]
rs4951609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951613	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs502502	0.92[JPT][hapmap]
rs510189	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs606996	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616408	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs678640	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72649991	0.84[EUR][1000 genomes]
rs72649993	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7553505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791561	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11119971	LOC642946	cis	multi-tissue	Pritchard
rs11119971	LQK1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212718600-212731400	Weak transcription	Right Atrium	heart
2	chr1:212723600-212730800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:212727400-212731200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:212728400-212731400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:212728600-212731400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:212728800-212731200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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