Variant report

Variant	rs10412858
Chromosome Location	chr19:18759279-18759280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18713980..18716446-chr19:18757354..18760125,2	K562	blood:
2	chr19:18757758..18761197-chr19:18765478..18769110,5	MCF-7	breast:
3	chr19:18758073..18760878-chr19:18781482..18783635,2	K562	blood:
4	chr19:18716960..18718504-chr19:18758671..18760840,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006016	Chromatin interaction
ENSG00000105696	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10221489	0.81[CHB][hapmap]
rs10412053	0.84[ASN][1000 genomes]
rs10419226	0.89[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10420228	0.82[ASN][1000 genomes]
rs10421503	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10423674	0.81[CHB][hapmap]
rs10424265	0.84[ASN][1000 genomes]
rs10854003	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11085236	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883401	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12976113	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1473116	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs2214524	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385178	0.83[ASN][1000 genomes]
rs3764627	0.86[ASN][1000 genomes]
rs3829671	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808145	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4808147	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6510995	0.83[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6510996	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7246437	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7257812	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs757347	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs757350	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8100824	0.89[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8102046	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs876982	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs886443	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs889364	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[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	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10412858	CCDC39	trans	parietal	SCAN
rs10412858	UBA52	cis	lymphoblastoid	seeQTL
rs10412858	DDA1	cis	parietal	SCAN
rs10412858	GDF1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18748400-18761600	Weak transcription	Aorta	Aorta
2	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:18749200-18759600	Weak transcription	Thymus	Thymus
4	chr19:18749200-18759800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:18749200-18768200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:18749400-18759400	Weak transcription	Fetal Intestine Large	intestine
8	chr19:18749400-18759600	Weak transcription	Liver	Liver
9	chr19:18749400-18759800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:18749400-18760000	Weak transcription	Fetal Brain Female	brain
11	chr19:18749400-18762200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:18749400-18774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr19:18749600-18759800	Weak transcription	Primary T cells from cord blood	blood
14	chr19:18749800-18760800	Weak transcription	Dnd41	blood
15	chr19:18751200-18759600	Weak transcription	Stomach Mucosa	stomach
16	chr19:18754800-18760000	Enhancers	Brain Substantia Nigra	brain
17	chr19:18755000-18759400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr19:18755400-18760000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr19:18755600-18759400	Weak transcription	Colonic Mucosa	Colon
20	chr19:18755600-18759400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr19:18755600-18762200	Weak transcription	NHEK	skin
22	chr19:18755800-18759400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr19:18755800-18760000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr19:18755800-18764000	Enhancers	Right Ventricle	heart
25	chr19:18755800-18766600	Weak transcription	HepG2	liver
26	chr19:18756000-18759400	Weak transcription	GM12878-XiMat	blood
27	chr19:18756000-18759600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:18756000-18759600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr19:18756000-18759600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:18756000-18759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr19:18756000-18760200	Weak transcription	Fetal Brain Male	brain
32	chr19:18756200-18759400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr19:18756200-18759600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:18756200-18759600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:18756200-18759600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr19:18756200-18759600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:18756200-18759600	Weak transcription	Ovary	ovary
38	chr19:18756200-18759800	Enhancers	Brain Hippocampus Middle	brain
39	chr19:18756200-18760000	Weak transcription	Brain Germinal Matrix	brain
40	chr19:18756400-18759400	Weak transcription	HMEC	breast
41	chr19:18756400-18759600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:18756400-18759600	Weak transcription	Osteobl	bone
43	chr19:18756400-18778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:18756600-18759400	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:18756600-18760000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:18756800-18759400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr19:18756800-18759600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr19:18756800-18760000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:18756800-18760000	Enhancers	Brain Anterior Caudate	brain
50	chr19:18757200-18760200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links