Variant report

Variant	rs10406271
Chromosome Location	chr19:57011493-57011494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC004696.1-1	chr19:57011463-57012035	ENSG00000166770.6

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10404464	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406535	0.80[EUR][1000 genomes]
rs10406985	0.80[EUR][1000 genomes]
rs10408108	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414817	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417966	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419553	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973457	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12981768	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12982001	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2189698	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv960764	chr19:57007653-57012055	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10406271	ZFP28	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57003000-57018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:57003200-57018400	Weak transcription	Osteobl	bone
3	chr19:57003600-57017000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:57003800-57011600	Weak transcription	Fetal Heart	heart
5	chr19:57006200-57018600	Weak transcription	Dnd41	blood
6	chr19:57007000-57016000	Weak transcription	HSMM	muscle
7	chr19:57007200-57018400	Weak transcription	HSMMtube	muscle
8	chr19:57007200-57018600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:57007400-57011600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:57007600-57018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:57007600-57018600	Weak transcription	Fetal Brain Male	brain
12	chr19:57007800-57011800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr19:57007800-57014200	Weak transcription	Pancreas	Pancrea
14	chr19:57007800-57014400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:57007800-57014600	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:57007800-57018600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:57007800-57018600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:57007800-57018600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:57007800-57018600	Weak transcription	Brain Germinal Matrix	brain
20	chr19:57007800-57018600	Weak transcription	Esophagus	oesophagus
21	chr19:57007800-57018600	Weak transcription	Fetal Kidney	kidney
22	chr19:57007800-57018600	Weak transcription	Fetal Muscle Leg	muscle
23	chr19:57007800-57018600	Weak transcription	Left Ventricle	heart
24	chr19:57007800-57018600	Weak transcription	Right Ventricle	heart
25	chr19:57007800-57019200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:57008000-57011600	Weak transcription	Brain Substantia Nigra	brain
27	chr19:57008000-57011600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:57008000-57018400	Weak transcription	Fetal Brain Female	brain
29	chr19:57008400-57018600	Weak transcription	Fetal Stomach	stomach
30	chr19:57008600-57018600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:57009000-57014200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:57009000-57018200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:57009600-57018200	Weak transcription	Brain Anterior Caudate	brain
34	chr19:57009800-57012000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:57009800-57014200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:57009800-57018400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:57009800-57018400	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr19:57010000-57018600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:57011000-57012400	ZNF genes & repeats	Ovary	ovary
40	chr19:57011200-57013200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr19:57011400-57011800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
42	chr19:57011400-57012000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:57011400-57012000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:57011400-57012000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:57011400-57012000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:57011400-57012200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr19:57011400-57012200	ZNF genes & repeats	Aorta	Aorta
48	chr19:57011400-57012400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr19:57011400-57012400	ZNF genes & repeats	Brain Angular Gyrus	brain
50	chr19:57011400-57015000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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