Variant report

Variant	rs2613961
Chromosome Location	chr3:112829161-112829162
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTPBP8-1	chr3:112828949-112829322	ENSG00000240057.1

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1461107	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1795168	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1795170	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1797623	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1797624	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1797625	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1797626	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2245698	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2613946	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2613948	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2700198	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2700200	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2700201	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2926813	0.87[AMR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv877344	chr3:112789865-112854339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877345	chr3:112826253-112848851	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112808800-112832400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:112819400-112830400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:112822200-112829400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:112824200-112829800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:112824400-112829400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:112824600-112829200	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:112825000-112829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:112825000-112829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:112825000-112829800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:112825200-112829800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:112825600-112829400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:112825800-112829400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:112826000-112832200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:112826200-112829800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:112827600-112830400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:112828000-112829800	Weak transcription	HMEC	breast
17	chr3:112828000-112830000	Enhancers	Ovary	ovary
18	chr3:112828000-112830200	Enhancers	Fetal Thymus	thymus
19	chr3:112828000-112830400	Enhancers	Fetal Muscle Leg	muscle
20	chr3:112828200-112829200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:112828200-112830000	Weak transcription	NHEK	skin
22	chr3:112828200-112836200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:112828600-112829800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:112828800-112830000	Enhancers	Fetal Muscle Trunk	muscle
25	chr3:112828800-112830200	Enhancers	Fetal Stomach	stomach

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