Variant report

Variant	rs2914381
Chromosome Location	chr19:53746553-53746554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VN1R4-2	chr19:53745464-53747264	NONHSAT067656

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10401578	0.82[CHB][hapmap]
rs10404048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10413453	0.89[ASN][1000 genomes]
rs10417666	0.82[ASN][1000 genomes]
rs11084227	0.82[CHB][hapmap]
rs1129002	0.88[CHB][hapmap]
rs12981894	0.89[ASN][1000 genomes]
rs12984188	0.87[CHB][hapmap]
rs12984473	0.87[CHB][hapmap]
rs17272966	0.87[CHB][hapmap]
rs2865241	0.85[ASN][1000 genomes]
rs2914371	0.83[CHB][hapmap]
rs2914372	0.80[CHB][hapmap]
rs2914373	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914374	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914376	0.87[CHB][hapmap]
rs2914378	0.87[CHB][hapmap]
rs2914379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914382	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914383	0.82[CHB][hapmap]
rs2965221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965226	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965227	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965232	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965233	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965234	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965235	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965239	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965241	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2965242	0.80[CHB][hapmap]
rs3097251	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111318	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111320	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239497	0.89[ASN][1000 genomes]
rs4801972	0.98[ASN][1000 genomes]
rs4803068	0.89[ASN][1000 genomes]
rs4803070	0.83[ASN][1000 genomes]
rs4803073	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803075	0.82[EUR][1000 genomes]
rs4803076	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803077	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247982	1.00[CHB][hapmap]
rs7248781	0.96[ASN][1000 genomes]
rs7248812	0.96[ASN][1000 genomes]
rs7249931	0.97[ASN][1000 genomes]
rs7253646	0.98[ASN][1000 genomes]
rs7257238	0.91[ASN][1000 genomes]
rs8104393	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104750	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105607	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109793	0.98[ASN][1000 genomes]
rs9788	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1064604	chr19:53730688-53751243	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv580079	chr19:53732590-53756120	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055236	chr19:53739483-53778339	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1059899	chr19:53744560-53768337	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1064070	chr19:53744560-53769702	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53728200-53748800	ZNF genes & repeats	Liver	Liver
2	chr19:53733600-53755200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:53733600-53755800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:53735800-53756200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:53736200-53749000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:53738600-53749000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:53738800-53756600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr19:53739400-53755200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:53739600-53748600	ZNF genes & repeats	Brain Anterior Caudate	brain
11	chr19:53739600-53748600	ZNF genes & repeats	Brain Germinal Matrix	brain
12	chr19:53739600-53756200	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:53740000-53747200	ZNF genes & repeats	Brain Substantia Nigra	brain
14	chr19:53740000-53749800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:53740000-53750600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:53740000-53756400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:53740000-53756600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
18	chr19:53740000-53756800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:53740200-53748800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr19:53740200-53748800	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr19:53740200-53749000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr19:53740200-53749000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr19:53740200-53749000	ZNF genes & repeats	Colon Smooth Muscle	Colon
24	chr19:53740200-53750600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
25	chr19:53740200-53752600	ZNF genes & repeats	Brain Hippocampus Middle	brain
26	chr19:53740200-53756800	ZNF genes & repeats	Fetal Lung	lung
27	chr19:53740200-53757600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:53740400-53747400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:53740400-53747800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
30	chr19:53740400-53747800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
31	chr19:53740400-53748600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
32	chr19:53740400-53748800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:53740400-53749000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr19:53740400-53749000	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr19:53740400-53749000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
36	chr19:53740400-53749000	ZNF genes & repeats	Dnd41	blood
37	chr19:53740400-53756800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr19:53740600-53747600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:53740600-53747800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
40	chr19:53740600-53748000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
41	chr19:53740600-53750600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
42	chr19:53740800-53748800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
43	chr19:53742600-53747600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
44	chr19:53742600-53747600	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr19:53742800-53747600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr19:53742800-53747800	ZNF genes & repeats	Psoas Muscle	Psoas
47	chr19:53742800-53748800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:53743000-53747000	ZNF genes & repeats	NH-A	brain
49	chr19:53743000-53747200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
50	chr19:53743000-53747400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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