Variant report

Variant	rs1496049
Chromosome Location	chr1:152161949-152161950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCE5A-2	chr1:152161827-152161984	ENSG00000237975

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10749669	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10749670	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs10788824	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788827	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788828	0.84[EUR][1000 genomes]
rs10888466	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888467	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888468	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888470	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs10888471	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10888473	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11204933	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11204937	0.83[EUR][1000 genomes]
rs11204938	0.83[EUR][1000 genomes]
rs11204939	0.82[EUR][1000 genomes]
rs11204947	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11204948	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11204949	0.80[CHB][hapmap]
rs11204978	0.91[CEU][hapmap];0.80[CHB][hapmap]
rs11204980	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11204981	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs11583524	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584340	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11584427	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs11586114	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs11587676	0.91[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes]
rs11588174	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11589532	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11589587	0.81[EUR][1000 genomes]
rs11590365	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12047544	0.82[ASN][1000 genomes]
rs12063165	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12116736	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117911	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12144058	0.81[ASN][1000 genomes]
rs12405278	0.81[CHB][hapmap]
rs12408581	0.81[EUR][1000 genomes]
rs12409762	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12567463	0.88[EUR][1000 genomes]
rs12748016	0.82[EUR][1000 genomes]
rs12749966	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1353436	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1390485	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1390487	0.84[EUR][1000 genomes]
rs1390488	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs1390490	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1496045	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1496050	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1496051	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1552992	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552993	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552995	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552996	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858480	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1858482	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs2065955	0.92[CEU][hapmap]
rs2184953	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2291770	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2338431	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2338555	0.91[CEU][hapmap];0.82[CHB][hapmap]
rs3120659	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap]
rs3126066	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3126085	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs3126088	0.91[CEU][hapmap];0.80[CHB][hapmap]
rs3126091	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4415568	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4421596	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4456098	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845421	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845423	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4845426	0.82[EUR][1000 genomes]
rs4845733	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845734	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845736	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845737	0.85[JPT][hapmap]
rs4845740	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845741	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845742	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845744	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845745	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845750	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs55982921	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56013982	0.81[EUR][1000 genomes]
rs6587647	0.84[EUR][1000 genomes]
rs6587651	0.84[EUR][1000 genomes]
rs6587652	0.83[EUR][1000 genomes]
rs6587666	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6662450	0.83[EUR][1000 genomes]
rs6666382	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs72696963	0.81[EUR][1000 genomes]
rs74127901	0.82[EUR][1000 genomes]
rs7520249	0.84[EUR][1000 genomes]
rs7531094	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7533529	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7534716	0.82[EUR][1000 genomes]
rs7535536	0.83[EUR][1000 genomes]
rs7550106	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs868303	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs868304	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs877776	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.82[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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv547854	chr1:152145661-152165878	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv528426	chr1:152161735-152162106	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1496049	FLG	cis	Thyroid	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152160600-152162000	Weak transcription	Hela-S3	cervix
2	chr1:152161000-152162000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:152161000-152162200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:152161000-152162200	Active TSS	Primary T cells from cord blood	blood
5	chr1:152161000-152162200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:152161000-152162200	Active TSS	Right Ventricle	heart
7	chr1:152161000-152162600	Active TSS	Stomach Smooth Muscle	stomach
8	chr1:152161200-152162000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:152161200-152162000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
11	chr1:152161200-152162000	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
13	chr1:152161200-152162000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr1:152161200-152162000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:152161200-152162000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:152161200-152162000	Active TSS	Muscle Satellite Cultured Cells	--
17	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:152161200-152162000	Active TSS	Aorta	Aorta
20	chr1:152161200-152162000	Active TSS	Esophagus	oesophagus
21	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
24	chr1:152161200-152162000	Flanking Active TSS	Lung	lung
25	chr1:152161200-152162000	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
26	chr1:152161200-152162000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr1:152161200-152162000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
28	chr1:152161200-152162200	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr1:152161200-152162200	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:152161200-152162200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr1:152161200-152162200	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr1:152161200-152162200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:152161200-152162200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:152161200-152162200	Active TSS	Brain Substantia Nigra	brain
35	chr1:152161200-152162200	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr1:152161200-152162200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
37	chr1:152161200-152162200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr1:152161200-152162200	Active TSS	Left Ventricle	heart
39	chr1:152161200-152162200	Active TSS	Ovary	ovary
40	chr1:152161200-152162200	Active TSS	Placenta Amnion	Placenta Amnion
41	chr1:152161200-152162200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
42	chr1:152161200-152162200	Active TSS	GM12878-XiMat	blood
43	chr1:152161200-152162200	Active TSS	HSMM	muscle
44	chr1:152161200-152162400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:152161200-152162400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr1:152161200-152162400	Active TSS	Brain Angular Gyrus	brain
47	chr1:152161200-152162400	Active TSS	Brain Cingulate Gyrus	brain
48	chr1:152161200-152162400	Active TSS	Brain Hippocampus Middle	brain
49	chr1:152161200-152162400	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:152161200-152162400	Active TSS	Colon Smooth Muscle	Colon

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