Variant report

Variant	rs10419281
Chromosome Location	chr19:37950253-37950254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37950211..37953608-chr19:37957437..37960728,3	MCF-7	breast:
2	chr19:37930059..37932507-chr19:37948156..37950930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171827	Chromatin interaction
ENSG00000196437	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1019494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10425719	0.88[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs11083423	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666708	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462546	0.91[ASN][1000 genomes]
rs12981359	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981830	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1545755	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs185368	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs185369	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1968251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	0.82[ASW][hapmap]
rs2306201	0.82[ASW][hapmap]
rs2385180	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385181	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431992	0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs256733	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs256735	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256740	0.84[ASN][1000 genomes]
rs256744	0.84[ASN][1000 genomes]
rs2927745	0.95[CHB][hapmap];0.81[CHD][hapmap]
rs34410821	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35470250	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4344867	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502546	0.86[JPT][hapmap]
rs55755939	0.82[ASN][1000 genomes]
rs6508721	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6508725	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247090	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7254009	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109103	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10419281	HIPK4	cis	parietal	SCAN
rs10419281	DMPK	cis	parietal	SCAN
rs10419281	CBLC	cis	parietal	SCAN
rs10419281	ZNF226	cis	cerebellum	SCAN
rs10419281	AC012309.5	cis	Esophagus Muscularis	GTEx
rs10419281	IL29	cis	parietal	SCAN
rs10419281	AC012309.5	cis	Thyroid	GTEx
rs10419281	AKT2	cis	parietal	SCAN
rs10419281	ZNF781	trans	cerebellum	SCAN
rs10419281	EIF3K	cis	parietal	SCAN
rs10419281	PHLDB3	cis	cerebellum	SCAN
rs10419281	AC012309.5	cis	Artery Tibial	GTEx
rs10419281	PLEKHG2	cis	cerebellum	SCAN
rs10419281	AC012309.5	cis	Heart Left Ventricle	GTEx
rs10419281	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37898000-37956400	ZNF genes & repeats	Liver	Liver
2	chr19:37910800-37956000	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:37911200-37954600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:37938000-37956000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37938200-37956200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:37938600-37951800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:37940800-37954200	ZNF genes & repeats	Brain Hippocampus Middle	brain
8	chr19:37940800-37956800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:37941000-37952200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
10	chr19:37942400-37954400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr19:37942400-37954600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:37942400-37956000	ZNF genes & repeats	Fetal Lung	lung
13	chr19:37942400-37956200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:37942400-37957200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:37942600-37953800	ZNF genes & repeats	Brain Substantia Nigra	brain
16	chr19:37942600-37956000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:37942600-37956600	ZNF genes & repeats	Dnd41	blood
18	chr19:37943400-37950600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr19:37943600-37953200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr19:37943600-37954000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr19:37943600-37956800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:37943800-37951600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:37944200-37957000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:37944600-37954000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:37944600-37954400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
26	chr19:37944600-37954800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
27	chr19:37944600-37956200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr19:37944600-37956400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:37944600-37957000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:37944800-37954000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:37944800-37954600	ZNF genes & repeats	Primary T cells from cord blood	blood
32	chr19:37944800-37956200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:37944800-37956200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
34	chr19:37944800-37957000	ZNF genes & repeats	A549	lung
35	chr19:37946200-37957400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:37946800-37951000	Weak transcription	Gastric	stomach
37	chr19:37946800-37951000	Weak transcription	Pancreas	Pancrea
38	chr19:37946800-37956800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:37946800-37957000	Weak transcription	NH-A	brain
40	chr19:37946800-37957200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:37947400-37953600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr19:37947600-37954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:37947600-37955600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:37948400-37953200	Weak transcription	Fetal Heart	heart
45	chr19:37948800-37951000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:37948800-37953200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
47	chr19:37948800-37954200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
48	chr19:37949000-37950400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
49	chr19:37949000-37950600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
50	chr19:37949000-37951000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links