Variant report

Variant	rs1650972
Chromosome Location	chr19:53643497-53643498
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	chr19:53636525..53638323-chr19:53641645..53644097,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VN1R2-8	chr19:53643081-53644210	NONHSAT067638
2	lnc-VN1R2-8	chr19:53643081-53644210	NONHSAT067639

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10408917	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12972886	0.99[EUR][1000 genomes]
rs1613687	0.84[CEU][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584269	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251457	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253161	0.99[EUR][1000 genomes]
rs9967643	0.85[EUR][1000 genomes]

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	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh 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
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv912350	chr19:53636016-53687818	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1650972	ZNF415	cis	Artery Tibial	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53636400-53643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:53636600-53643600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:53636600-53643600	Weak transcription	Brain Angular Gyrus	brain
4	chr19:53636600-53643600	Weak transcription	Brain Hippocampus Middle	brain
5	chr19:53636600-53644600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:53636600-53644600	Weak transcription	Fetal Brain Male	brain
7	chr19:53636600-53645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr19:53636800-53643800	Weak transcription	Brain Germinal Matrix	brain
9	chr19:53636800-53643800	Weak transcription	Dnd41	blood
10	chr19:53640000-53660600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:53640600-53655800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:53642000-53646400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:53642000-53653600	ZNF genes & repeats	Liver	Liver
14	chr19:53642200-53645800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:53642200-53645800	ZNF genes & repeats	HSMM	muscle
16	chr19:53642200-53646400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:53642200-53646400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
18	chr19:53642200-53654600	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr19:53642400-53646200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:53642400-53646400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:53642400-53653800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:53642400-53654000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr19:53642600-53645400	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
24	chr19:53642600-53646400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr19:53642800-53645800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr19:53642800-53648600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
27	chr19:53642800-53654600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:53642800-53655600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr19:53643000-53643600	ZNF genes & repeats	Placenta	Placenta
30	chr19:53643000-53645000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:53643000-53645200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:53643000-53646400	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr19:53643000-53646400	ZNF genes & repeats	Colonic Mucosa	Colon
34	chr19:53643000-53654600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
35	chr19:53643200-53643600	Weak transcription	Fetal Brain Female	brain
36	chr19:53643200-53643600	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:53643200-53646200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
38	chr19:53643200-53646400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
39	chr19:53643200-53646400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
40	chr19:53643200-53646600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr19:53643200-53648400	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr19:53643400-53643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:53643400-53644400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:53643400-53646000	ZNF genes & repeats	Aorta	Aorta
45	chr19:53643400-53646200	ZNF genes & repeats	NH-A	brain
46	chr19:53643400-53646400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr19:53643400-53646400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:53643400-53646400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:53643400-53646400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:53643400-53646400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links