Variant report

Variant	rs2887290
Chromosome Location	chr19:40821506-40821507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40794373..40797365-chr19:40820678..40822952,2	K562	blood:
2	chr19:40814675..40816764-chr19:40819751..40822221,2	K562	blood:
3	chr19:40821045..40823190-chr19:40827366..40829616,2	MCF-7	breast:
4	chr19:40817646..40819198-chr19:40820756..40822692,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLD3-3	chr19:40819394-40825438	NONHSAT066371

Variant related genes	Relation type
ENSG00000160392	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs16974071	1.00[AMR][1000 genomes]
rs2126122	1.00[AMR][1000 genomes]
rs55869814	1.00[AMR][1000 genomes]
rs58622948	1.00[AMR][1000 genomes]
rs73930697	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv3386713	chr19:40794161-40828617	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40792000-40826200	Weak transcription	Hela-S3	cervix
2	chr19:40793000-40822000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:40793200-40822000	Weak transcription	Fetal Stomach	stomach
4	chr19:40793800-40821800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:40800400-40826400	Weak transcription	Brain Angular Gyrus	brain
6	chr19:40800800-40822000	Weak transcription	Brain Hippocampus Middle	brain
7	chr19:40802800-40828000	Weak transcription	NH-A	brain
8	chr19:40803000-40822000	Weak transcription	Lung	lung
9	chr19:40803800-40822000	Weak transcription	Primary T cells from cord blood	blood
10	chr19:40807600-40822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:40808800-40822000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr19:40809000-40822000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:40810600-40825800	Weak transcription	Adipose Nuclei	Adipose
14	chr19:40810600-40829800	Weak transcription	NHDF-Ad	bronchial
15	chr19:40810800-40826200	Weak transcription	HMEC	breast
16	chr19:40811200-40821800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:40811200-40821800	Weak transcription	Liver	Liver
18	chr19:40811200-40822200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:40811200-40822200	Weak transcription	Thymus	Thymus
20	chr19:40811200-40826000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:40811400-40826600	Weak transcription	NHEK	skin
22	chr19:40811600-40826600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:40811800-40822200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr19:40811800-40822200	Weak transcription	A549	lung
25	chr19:40811800-40826400	Weak transcription	Brain Substantia Nigra	brain
26	chr19:40811800-40826600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:40811800-40826600	Weak transcription	Fetal Lung	lung
28	chr19:40811800-40831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:40813200-40822000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:40814200-40821800	Weak transcription	Placenta	Placenta
31	chr19:40814600-40824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:40815400-40832800	Weak transcription	Fetal Brain Male	brain
33	chr19:40815600-40826000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:40815800-40824400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr19:40816000-40822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:40816400-40824200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:40817200-40825800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr19:40817400-40827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:40817600-40827200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr19:40817800-40822000	Weak transcription	Spleen	Spleen
41	chr19:40818600-40822000	Weak transcription	Right Ventricle	heart
42	chr19:40818800-40824200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:40819000-40822200	Weak transcription	Fetal Muscle Leg	muscle
44	chr19:40819000-40824400	Weak transcription	GM12878-XiMat	blood
45	chr19:40819200-40825800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr19:40819200-40826800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:40819200-40834000	Weak transcription	Fetal Kidney	kidney
48	chr19:40819400-40824400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:40819400-40828200	Weak transcription	Osteobl	bone
50	chr19:40819600-40822000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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