Variant report

Variant	rs1539497
Chromosome Location	chr1:224150723-224150724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12568004	0.81[AMR][1000 genomes]
rs1539496	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3991971	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61825422	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61825443	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61826580	0.82[EUR][1000 genomes]
rs61826582	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61826584	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61826596	0.81[AMR][1000 genomes]
rs61826599	0.81[AMR][1000 genomes]
rs61826602	0.81[AMR][1000 genomes]
rs61826603	0.81[AMR][1000 genomes]
rs61826608	0.81[AMR][1000 genomes]
rs61826610	0.81[AMR][1000 genomes]
rs72629693	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9219	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv873214	chr1:224075483-224166332	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873215	chr1:224075483-224204433	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv873216	chr1:224075483-224230307	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1802502	chr1:224076065-224184733	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1796263	chr1:224077300-224171777	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1819762	chr1:224077300-224171777	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv873217	chr1:224089383-224190316	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	esv15701	chr1:224096726-224179951	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv873218	chr1:224097155-224204433	Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv873219	chr1:224097155-224216822	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv873220	chr1:224097155-224223659	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv549241	chr1:224103992-224216757	Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv873221	chr1:224115297-224183599	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv549242	chr1:224115297-224203918	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
18	nsv549243	chr1:224115297-224216757	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv945316	chr1:224133366-224196526	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv947067	chr1:224140479-224152588	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1539497	RP11-504P24.6	cis	Thyroid	GTEx
rs1539497	RP11-504P24.3	cis	Nerve Tibial	GTEx
rs1539497	RP11-504P24.6	cis	Nerve Tibial	GTEx
rs1539497	RP11-504P24.4	cis	Thyroid	GTEx
rs1539497	RP11-504P24.4	cis	Nerve Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224136400-224179800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:224137800-224160600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:224138000-224162800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:224138000-224163800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:224138000-224170000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:224138000-224179600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:224138200-224179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:224138200-224179600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:224138200-224179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:224138400-224179600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:224138400-224179800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:224138600-224179600	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:224138800-224179800	Weak transcription	Left Ventricle	heart
14	chr1:224139800-224152800	Weak transcription	Spleen	Spleen
15	chr1:224139800-224158400	Weak transcription	Lung	lung
16	chr1:224139800-224161000	Weak transcription	Adipose Nuclei	Adipose
17	chr1:224139800-224163200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:224139800-224174000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:224139800-224179600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:224140000-224170000	Weak transcription	Fetal Intestine Small	intestine
21	chr1:224140200-224179800	Weak transcription	Placenta	Placenta
22	chr1:224140400-224152600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:224140400-224160600	Weak transcription	Ovary	ovary
24	chr1:224140400-224179200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:224140400-224179800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:224140600-224160600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:224141400-224179200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:224145000-224179800	Weak transcription	Primary T cells from cord blood	blood
29	chr1:224146800-224179600	Weak transcription	Fetal Intestine Large	intestine
30	chr1:224148600-224163200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:224150000-224179800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:224150000-224179800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:224150200-224179800	Weak transcription	Liver	Liver
34	chr1:224150400-224158000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:224150400-224173200	Weak transcription	Fetal Stomach	stomach

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