Variant report

Variant	rs10415278
Chromosome Location	chr19:19769157-19769158
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19769006-19769271	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:19769139-19769165	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19761051..19765216-chr19:19766866..19770824,5	K562	blood:
2	chr19:19753683..19755957-chr19:19767700..19769779,2	K562	blood:
3	chr19:19763068..19765978-chr19:19768250..19769834,2	MCF-7	breast:
4	chr19:19767560..19771032-chr19:19771876..19774701,8	MCF-7	breast:
5	chr19:19752450..19756333-chr19:19763709..19769200,7	K562	blood:

No data

Variant related genes	Relation type
ATP13A1	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10401926	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10403579	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10421328	0.88[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes]
rs10423449	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668721	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11671684	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2288865	0.88[CEU][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs2288867	0.83[CEU][hapmap];0.83[TSI][hapmap]
rs34174818	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55831814	0.81[EUR][1000 genomes]
rs56236407	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7253821	0.94[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73006705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs867616	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884480	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs919778	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv911310	chr19:19753882-19784891	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	esv3330851	chr19:19755507-19852881	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10415278	UNC13A	cis	cerebellum	SCAN
rs10415278	GMIP	cis	parietal	SCAN
rs10415278	C21orf128	trans	cerebellum	SCAN
rs10415278	ZNF14	cis	parietal	SCAN
rs10415278	ZNF14	cis	cerebellum	SCAN
rs10415278	ZNF714	cis	parietal	SCAN
rs10415278	ZNF101	cis	parietal	SCAN
rs10415278	C19orf60	cis	parietal	SCAN
rs10415278	SNORA68	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19754800-19772400	Weak transcription	Right Atrium	heart
2	chr19:19755000-19769600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:19755000-19770800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:19755000-19771000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:19755000-19771200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:19755000-19771200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:19755000-19772000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:19755000-19772200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:19755200-19770600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:19755200-19770600	Strong transcription	Dnd41	blood
12	chr19:19755200-19770800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:19755200-19770800	Strong transcription	Adipose Nuclei	Adipose
14	chr19:19755200-19770800	Strong transcription	Brain Germinal Matrix	brain
15	chr19:19755200-19770800	Strong transcription	Fetal Intestine Large	intestine
16	chr19:19755200-19770800	Strong transcription	Spleen	Spleen
17	chr19:19755200-19771000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:19755200-19771000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:19755200-19771000	Strong transcription	Fetal Lung	lung
20	chr19:19755200-19771000	Strong transcription	Placenta	Placenta
21	chr19:19755200-19771200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr19:19755200-19771200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:19755200-19771200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr19:19755200-19771600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:19755200-19771600	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:19755200-19772200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:19755200-19772200	Strong transcription	Fetal Stomach	stomach
28	chr19:19755200-19772200	Strong transcription	NHEK	skin
29	chr19:19755200-19772400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:19755400-19770600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr19:19755400-19770800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr19:19755400-19771000	Strong transcription	Osteobl	bone
33	chr19:19755400-19771200	Strong transcription	Fetal Thymus	thymus
34	chr19:19755400-19771200	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:19755400-19772800	Strong transcription	Thymus	Thymus
36	chr19:19755600-19770800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:19755600-19771000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:19755600-19771000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr19:19755600-19771000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:19755600-19771000	Strong transcription	Liver	Liver
41	chr19:19755600-19771200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr19:19755600-19771200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:19755600-19771200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr19:19755600-19771200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr19:19755600-19771400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:19755600-19772200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:19755600-19772400	Strong transcription	Fetal Intestine Small	intestine
48	chr19:19755800-19770400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:19755800-19771000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:19755800-19771200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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