Variant report

Variant	rs10423565
Chromosome Location	chr19:39889044-39889045
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39888709..39889395-chr19:39897215..39898083,2	MCF-7	breast:
2	chr19:39887250..39889651-chr19:39901829..39904000,29	K562	blood:
3	chr19:39699475..39701716-chr19:39889022..39890849,2	MCF-7	breast:
4	chr19:39879787..39883867-chr19:39884525..39889123,13	K562	blood:
5	chr19:39887866..39890343-chr19:40030809..40032954,2	MCF-7	breast:
6	chr19:39832883..39834825-chr19:39888333..39890047,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128016	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000006712	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10402122	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10403504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10412877	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10414216	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10425594	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11665856	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672863	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12973448	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12977767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs251864	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3843755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803235	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs565545	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7250966	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253005	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7256692	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS 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	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10423565	IXL	cis	multi-tissue	Pritchard
rs10423565	MED29	cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39883000-39891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39883200-39891600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:39883200-39892400	Weak transcription	Fetal Brain Male	brain
4	chr19:39883200-39892400	Weak transcription	Fetal Kidney	kidney
5	chr19:39884200-39889600	Strong transcription	Brain Germinal Matrix	brain
6	chr19:39885000-39892600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:39886200-39892000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:39886200-39892400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:39886800-39893400	Weak transcription	Aorta	Aorta
10	chr19:39886800-39893400	Weak transcription	Ovary	ovary
11	chr19:39887800-39889600	Genic enhancers	Pancreas	Pancrea
12	chr19:39887800-39889600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr19:39887800-39889600	Genic enhancers	Spleen	Spleen
14	chr19:39887800-39889800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:39887800-39889800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr19:39887800-39890600	Genic enhancers	Fetal Thymus	thymus
17	chr19:39888000-39889200	Genic enhancers	Fetal Stomach	stomach
18	chr19:39888000-39889400	Enhancers	Psoas Muscle	Psoas
19	chr19:39888000-39889600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:39888000-39889600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
21	chr19:39888000-39889600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:39888000-39889600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:39888000-39889600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:39888000-39889600	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr19:39888000-39889600	Genic enhancers	Fetal Muscle Leg	muscle
26	chr19:39888000-39889600	Enhancers	Left Ventricle	heart
27	chr19:39888000-39889600	Genic enhancers	Dnd41	blood
28	chr19:39888000-39889800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:39888000-39889800	Enhancers	HMEC	breast
30	chr19:39888000-39890400	Genic enhancers	Placenta	Placenta
31	chr19:39888000-39890600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:39888000-39891000	Genic enhancers	Fetal Intestine Small	intestine
33	chr19:39888000-39892400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr19:39888000-39893600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:39888000-39893600	Enhancers	Stomach Mucosa	stomach
36	chr19:39888200-39889200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:39888200-39889200	Enhancers	HUVEC	blood vessel
38	chr19:39888200-39889600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr19:39888200-39889600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:39888200-39889600	Enhancers	Gastric	stomach
41	chr19:39888200-39889600	Flanking Active TSS	Hela-S3	cervix
42	chr19:39888200-39889600	Enhancers	NH-A	brain
43	chr19:39888200-39889800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr19:39888200-39889800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:39888200-39889800	Enhancers	HSMMtube	muscle
46	chr19:39888200-39889800	Enhancers	NHDF-Ad	bronchial
47	chr19:39888200-39890400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:39888200-39892000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:39888200-39892000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:39888200-39892600	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links