Variant report

Variant	rs11847588
Chromosome Location	chr14:56025646-56025647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56022620..56026445-chr14:56044953..56047966,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBPL2-1	chr14:56024690-56026492	ENSG00000186615
2	lnc-TBPL2-1	chr14:56024690-56026492	XLOC_011036

Variant related genes	Relation type
ENSG00000186615	Chromatin interaction
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11847813	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12886742	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12890794	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12890934	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12894700	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17128552	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17128557	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1951892	0.87[ASN][1000 genomes]
rs1951893	0.89[ASN][1000 genomes]
rs2181742	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2181743	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2341884	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825617	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143891	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898868	0.91[ASN][1000 genomes]
rs4901578	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4901579	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4901580	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4901581	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4901582	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4901584	0.90[ASN][1000 genomes]
rs4901586	0.90[ASN][1000 genomes]
rs55823239	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6573037	0.90[ASN][1000 genomes]
rs6573040	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8017185	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9796397	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic 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	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1047054	chr14:55922287-56035579	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1037161	chr14:55928030-56039353	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56010600-56026600	Weak transcription	Right Ventricle	heart
2	chr14:56014000-56031200	Weak transcription	Left Ventricle	heart
3	chr14:56021000-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:56022600-56026600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr14:56023600-56045200	Weak transcription	Primary T cells from cord blood	blood
6	chr14:56024000-56028800	Weak transcription	HSMM	muscle
7	chr14:56024000-56043200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr14:56024200-56038200	Weak transcription	Brain Hippocampus Middle	brain
9	chr14:56024200-56045400	Weak transcription	Adipose Nuclei	Adipose
10	chr14:56024400-56026000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:56024400-56026600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:56024400-56028400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr14:56024400-56028800	Weak transcription	HSMMtube	muscle
14	chr14:56024400-56029000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr14:56024400-56029200	Weak transcription	Brain Anterior Caudate	brain
16	chr14:56024400-56032400	Weak transcription	Fetal Kidney	kidney
17	chr14:56024400-56035200	Weak transcription	A549	lung
18	chr14:56024400-56038200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr14:56024400-56039000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:56024400-56039400	Weak transcription	Brain Angular Gyrus	brain
21	chr14:56024400-56039400	Weak transcription	Fetal Stomach	stomach
22	chr14:56024400-56039600	Weak transcription	Pancreas	Pancrea
23	chr14:56024400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr14:56024400-56043600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:56024400-56043600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr14:56024400-56043600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:56024400-56045200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:56024400-56045200	Weak transcription	Ovary	ovary
29	chr14:56024400-56045400	Weak transcription	Hela-S3	cervix
30	chr14:56024400-56045400	Weak transcription	Osteobl	bone
31	chr14:56024400-56045800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:56024600-56025800	Weak transcription	NHEK	skin
33	chr14:56024600-56027600	Enhancers	Fetal Heart	heart
34	chr14:56024600-56043800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr14:56024600-56045400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:56025000-56027800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr14:56025000-56037000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr14:56025200-56028000	Weak transcription	Fetal Brain Male	brain
39	chr14:56025200-56045600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr14:56025600-56025800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr14:56025600-56025800	Enhancers	Fetal Muscle Leg	muscle
42	chr14:56025600-56026000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr14:56025600-56026200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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