Variant report

Variant	rs942099
Chromosome Location	chr1:78636879-78636880
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FUBP1-4	chr1:78636165-78636921	NONHSAT004068

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11799753	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804237	0.93[ASN][1000 genomes]
rs11806671	0.80[ASN][1000 genomes]
rs11807462	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807476	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808942	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410030	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335482	0.93[ASN][1000 genomes]
rs1407749	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17101469	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17101472	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17101475	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208968	0.80[ASN][1000 genomes]
rs3811442	0.93[ASN][1000 genomes]
rs4650471	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650481	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530042	1.00[ASN][1000 genomes]
rs55672379	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682319	0.93[ASN][1000 genomes]
rs699010	1.00[ASN][1000 genomes]
rs72687184	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687185	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687187	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687190	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72687200	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72688718	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7516182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529494	0.80[ASN][1000 genomes]
rs7532039	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532135	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535444	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7537442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537720	0.80[ASN][1000 genomes]
rs7547287	0.80[ASN][1000 genomes]
rs7554427	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850497	chr1:78596312-78645701	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78625200-78644400	Weak transcription	Pancreas	Pancrea
2	chr1:78632000-78637200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:78634400-78637600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:78634600-78637000	Weak transcription	HSMM	muscle
5	chr1:78634600-78637200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:78634600-78637600	Weak transcription	NHDF-Ad	bronchial
7	chr1:78634800-78637600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:78635000-78637200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:78635000-78646200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:78636000-78637600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:78636200-78637000	Enhancers	Colon Smooth Muscle	Colon
12	chr1:78636600-78637000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:78636600-78637000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:78636600-78638600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:78636800-78637400	Enhancers	NHEK	skin
16	chr1:78636800-78637600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:78636800-78637600	Enhancers	HMEC	breast
18	chr1:78636800-78637600	Enhancers	Osteobl	bone
19	chr1:78636800-78637800	Enhancers	Fetal Stomach	stomach
20	chr1:78636800-78638400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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