Variant report

Variant	rs4654050
Chromosome Location	chr1:224776165-224776166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224776063-224776306	NONHSAT009816
2	lnc-CNIH3-2	chr1:224776063-224776318	NONHSAT009801
3	lnc-CNIH3-2	chr1:224776063-224776194	NONHSAT009813
4	lnc-CNIH3-2	chr1:224776063-224776257	NONHSAT009815

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1002131	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10799586	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916644	0.97[EUR][1000 genomes]
rs10916645	0.97[EUR][1000 genomes]
rs10916647	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916648	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10916649	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916655	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10916656	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12042245	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12042501	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044182	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12044602	1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12046431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12047290	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134248	0.97[EUR][1000 genomes]
rs12136356	0.95[EUR][1000 genomes]
rs12145617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1909442	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2173526	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2405312	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653590	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4654048	0.97[EUR][1000 genomes]
rs4654053	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4654054	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4654059	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57674260	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59391065	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61825844	0.90[EUR][1000 genomes]
rs6426142	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6667012	0.97[EUR][1000 genomes]
rs6681385	0.97[EUR][1000 genomes]
rs6696059	0.97[EUR][1000 genomes]
rs873691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs883114	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9919286	0.84[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv873224	chr1:224746577-224794913	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4654050	LEFTY1	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224753600-224780400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:224767400-224779600	Weak transcription	HMEC	breast
3	chr1:224767600-224779800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:224767800-224780200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:224768000-224776400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224768000-224776600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:224768000-224776800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:224768000-224780400	Weak transcription	Psoas Muscle	Psoas
9	chr1:224768800-224779600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:224775800-224777000	Enhancers	Fetal Brain Male	brain
11	chr1:224775800-224777600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:224775800-224777600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:224776000-224776400	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:224776000-224776600	Enhancers	Fetal Brain Female	brain
15	chr1:224776000-224777400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:224776000-224777400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:224776000-224777400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:224776000-224777400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:224776000-224777600	Enhancers	HUES64 Cell Line	embryonic stem cell

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