Variant report

Variant	rs11590369
Chromosome Location	chr1:152903603-152903604
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRR2D-1	chr1:152902516-152904287	XLOC_001030

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10494282	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888529	0.84[CEU][hapmap]
rs1108410	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs11205181	0.88[CHB][hapmap]
rs11205182	0.81[CEU][hapmap]
rs11488175	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs11576457	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11576797	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs11576882	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577384	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578914	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580565	0.81[JPT][hapmap]
rs11581802	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11587269	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11588463	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590835	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs11812015	0.81[CEU][hapmap]
rs12041126	0.89[EUR][1000 genomes]
rs12079087	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs12083211	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs12734348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1415972	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs1500937	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs16834767	1.00[YRI][hapmap]
rs16834770	1.00[YRI][hapmap]
rs17627288	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995308	0.81[CEU][hapmap]
rs2050673	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2068678	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339386	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28462230	0.97[ASN][1000 genomes]
rs28608883	0.91[ASN][1000 genomes]
rs28924721	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs4620471	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959888	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241316	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56335979	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58124215	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58298199	0.97[EUR][1000 genomes]
rs61815707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815711	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61815713	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61815714	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815715	0.97[ASN][1000 genomes]
rs6587724	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs6661932	0.98[EUR][1000 genomes]
rs6663448	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664380	0.84[CEU][hapmap]
rs6665728	0.97[ASN][1000 genomes]
rs6673356	0.84[CEU][hapmap]
rs6675009	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs6686526	0.84[CEU][hapmap];0.88[CHB][hapmap]
rs6692062	0.81[CEU][hapmap]
rs6693927	0.84[CEU][hapmap]
rs7531076	0.82[CHB][hapmap]
rs7541328	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543689	0.81[CEU][hapmap]
rs7548977	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs7551014	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv831592	chr1:152815054-152997162	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv998873	chr1:152869127-152975258	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
8	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152896800-152905200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:152903400-152904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:152903400-152904400	Weak transcription	HMEC	breast

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