Variant report

Variant	rs10425040
Chromosome Location	chr19:44900988-44900989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF229-1	chr19:44900827-44901421	NONHSAT066696

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11881044	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151055	0.86[ASN][1000 genomes]
rs12709876	0.81[AMR][1000 genomes]
rs12971572	0.82[AMR][1000 genomes]
rs12973197	0.97[ASN][1000 genomes]
rs12973212	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1816464	0.86[ASN][1000 genomes]
rs1816465	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1816466	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1816467	0.98[ASN][1000 genomes]
rs2164114	0.92[ASN][1000 genomes]
rs2437013	0.98[ASN][1000 genomes]
rs2437014	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2437022	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2466414	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2466415	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571093	0.81[AMR][1000 genomes]
rs2571097	0.81[AMR][1000 genomes]
rs2571121	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571122	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2571123	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571124	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571125	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571126	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571127	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2571128	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571129	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571130	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571131	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571132	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571134	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571136	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2571141	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571143	0.82[ASN][1000 genomes]
rs2571144	0.93[ASN][1000 genomes]
rs2571145	0.94[ASN][1000 genomes]
rs2571147	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571148	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571149	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2571150	0.99[ASN][1000 genomes]
rs2571151	0.99[ASN][1000 genomes]
rs2571152	0.97[ASN][1000 genomes]
rs2571153	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2571154	0.80[EUR][1000 genomes]
rs2571155	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2722646	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2722647	0.87[ASN][1000 genomes]
rs2722648	0.86[EUR][1000 genomes]
rs2722650	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722652	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2722653	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2722658	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722659	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2722660	1.00[ASN][1000 genomes]
rs2722661	0.98[ASN][1000 genomes]
rs2722662	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722664	0.98[ASN][1000 genomes]
rs2722665	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2722667	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2722669	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28696788	0.89[ASN][1000 genomes]
rs35650732	0.97[ASN][1000 genomes]
rs4268861	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4305190	0.81[AMR][1000 genomes]
rs8102685	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs892593	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912110	chr19:44840789-44902190	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv912111	chr19:44852134-44902190	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv579855	chr19:44852134-44930348	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv515911	chr19:44852134-44935019	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv912113	chr19:44858776-44928885	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1062330	chr19:44863939-44938277	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
10	nsv960889	chr19:44877441-44913480	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv2763206	chr19:44885379-44941728	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv960852	chr19:44890187-44921203	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3318557	chr19:44892181-44938875	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv3318558	chr19:44892356-44938748	Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv15098	chr19:44892380-44913200	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv9734	chr19:44892761-44940023	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv2756827	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv2758764	chr19:44894102-44947444	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1065783	chr19:44894164-44930803	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1055278	chr19:44896386-44907795	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1063780	chr19:44896386-44930803	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1059267	chr19:44896386-44938277	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv1055870	chr19:44896386-44938779	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	esv2421963	chr19:44896398-44938791	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv442465	chr19:44896398-44938791	ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv1058295	chr19:44896888-44938779	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv1065703	chr19:44898759-44938779	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
28	esv2754816	chr19:44899473-44930803	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv1065424	chr19:44899546-44938779	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10425040	ZNF285	cis	Nerve Tibial	GTEx
rs10425040	ZNF285	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44888200-44904800	Weak transcription	Fetal Brain Male	brain
2	chr19:44889000-44905000	Weak transcription	Right Ventricle	heart
3	chr19:44889800-44904800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:44890200-44904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:44890200-44904800	Weak transcription	HSMMtube	muscle
6	chr19:44890600-44905000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:44891400-44905200	Weak transcription	Gastric	stomach
8	chr19:44892200-44905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:44892400-44901400	Weak transcription	A549	lung
10	chr19:44892400-44905000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:44893200-44905000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:44893600-44905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:44893800-44905200	Weak transcription	Thymus	Thymus
14	chr19:44894600-44905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:44895000-44905000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:44895200-44904800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:44896000-44905000	Weak transcription	Osteobl	bone
18	chr19:44896400-44905200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:44897200-44905000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:44897600-44905200	Weak transcription	HUVEC	blood vessel
21	chr19:44898800-44901000	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr19:44898800-44901000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
23	chr19:44898800-44901000	ZNF genes & repeats	Fetal Brain Female	brain
24	chr19:44898800-44901200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:44898800-44901200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
26	chr19:44898800-44901200	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:44898800-44901800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr19:44898800-44902400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:44898800-44902600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr19:44898800-44902800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:44899000-44901200	ZNF genes & repeats	Ovary	ovary
32	chr19:44899000-44901600	ZNF genes & repeats	Adipose Nuclei	Adipose
33	chr19:44899000-44901600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:44899000-44901800	ZNF genes & repeats	Fetal Lung	lung
35	chr19:44899000-44903000	ZNF genes & repeats	Liver	Liver
36	chr19:44899200-44901000	ZNF genes & repeats	Brain Anterior Caudate	brain
37	chr19:44899200-44901400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
38	chr19:44899200-44902800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr19:44899400-44901200	Strong transcription	Brain Hippocampus Middle	brain
40	chr19:44899400-44901800	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr19:44899600-44901200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:44899600-44905200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:44899800-44901000	Strong transcription	Fetal Muscle Leg	muscle
44	chr19:44899800-44901200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:44899800-44901200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr19:44899800-44901200	Strong transcription	Fetal Stomach	stomach
47	chr19:44899800-44901200	ZNF genes & repeats	Left Ventricle	heart
48	chr19:44899800-44901400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
49	chr19:44900000-44901600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
50	chr19:44900200-44901000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links