Variant report

Variant	rs10426809
Chromosome Location	chr19:39186950-39186951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39186779-39187727	A549	lung:	n/a	n/a
2	GATA2	chr19:39186682-39187010	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr19:39186808-39187452	K562	blood:	n/a	n/a
4	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
5	EP300	chr19:39186692-39186962	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a
7	EP300	chr19:39186024-39187337	SK-N-SH	brain:	n/a	chr19:39186087-39186101

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39147345..39151436-chr19:39186794..39189528,4	MCF-7	breast:
2	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
3	chr19:39138523..39140203-chr19:39185373..39187199,2	MCF-7	breast:
4	chr19:39185846..39187379-chr19:39189752..39191366,2	K562	blood:
5	chr19:39183521..39187102-chr19:39327849..39329398,3	MCF-7	breast:
6	chr19:39182129..39185762-chr19:39186877..39189539,4	MCF-7	breast:
7	chr19:39185891..39187427-chr19:39211415..39213129,2	K562	blood:
8	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267375	TF binding region
ENSG00000130402	Chromatin interaction
ENSG00000267375	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10403540	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs10415219	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs10424568	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs11083473	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11083475	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs11665964	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs16972767	0.83[CHD][hapmap];0.80[JPT][hapmap]
rs2279144	0.81[CHD][hapmap]
rs28377909	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3745859	0.85[CHD][hapmap]
rs3786835	0.80[JPT][hapmap];0.88[YRI][hapmap]
rs3786845	0.81[CHD][hapmap]
rs3786851	0.83[CHD][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs749701	0.88[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs755690	0.83[EUR][1000 genomes]
rs883433	0.83[CHD][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap]
rs9304577	0.82[CEU][hapmap]
rs979971	0.82[CHD][hapmap];0.80[JPT][hapmap]
rs979972	0.80[JPT][hapmap];0.88[YRI][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	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10426809	ERCC1	cis	cerebellum	SCAN
rs10426809	ZNF526	cis	cerebellum	SCAN
rs10426809	RPS16	cis	parietal	SCAN
rs10426809	LGALS17A	cis	cerebellum	SCAN
rs10426809	EXOSC5	cis	parietal	SCAN
rs10426809	PSG3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:39178600-39187800	Enhancers	Left Ventricle	heart
4	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
6	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:39180000-39192400	Genic enhancers	Lung	lung
10	chr19:39180800-39187000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
12	chr19:39182200-39187800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:39182200-39192600	Enhancers	Liver	Liver
14	chr19:39182200-39193400	Enhancers	Right Atrium	heart
15	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
16	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr19:39182400-39187000	Enhancers	Stomach Mucosa	stomach
19	chr19:39182400-39189600	Enhancers	Brain Angular Gyrus	brain
20	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
21	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
22	chr19:39182600-39190800	Genic enhancers	HepG2	liver
23	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
24	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
25	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
26	chr19:39183200-39188800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
27	chr19:39183400-39187000	Enhancers	Primary B cells from cord blood	blood
28	chr19:39183400-39187600	Enhancers	Small Intestine	intestine
29	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
30	chr19:39183800-39188200	Weak transcription	Fetal Brain Female	brain
31	chr19:39184000-39187200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:39184200-39187800	Weak transcription	Fetal Brain Male	brain
33	chr19:39184400-39187200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr19:39184400-39187600	Weak transcription	K562	blood
35	chr19:39184400-39189200	Weak transcription	Brain Germinal Matrix	brain
36	chr19:39184400-39190200	Enhancers	Brain Anterior Caudate	brain
37	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
38	chr19:39184600-39187200	Enhancers	Right Ventricle	heart
39	chr19:39184600-39188800	Genic enhancers	NHEK	skin
40	chr19:39184800-39187000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:39184800-39187000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:39184800-39187800	Genic enhancers	HMEC	breast
43	chr19:39184800-39188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr19:39184800-39188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:39184800-39188600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:39184800-39188600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:39184800-39188800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr19:39184800-39189600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr19:39184800-39190000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:39184800-39190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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