Variant report

Variant	rs870218
Chromosome Location	chr19:38771175-38771176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38759485..38762494-chr19:38770790..38773902,4	K562	blood:
2	chr19:38771059..38771781-chr19:38789868..38790376,2	MCF-7	breast:
3	chr19:38770173..38772306-chr19:38806423..38808075,2	K562	blood:
4	chr19:38770260..38772183-chr19:38775620..38777576,2	K562	blood:

Variant related genes	Relation type
ENSG00000167645	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11666449	0.85[TSI][hapmap]
rs11669230	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11672219	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11672531	0.90[GIH][hapmap];0.88[MEX][hapmap]
rs11673222	0.88[MEX][hapmap]
rs2304177	0.90[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35308902	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3745951	0.87[MEX][hapmap]
rs3816044	0.90[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs3900981	0.82[GIH][hapmap];0.89[TSI][hapmap]
rs4386247	0.88[MEX][hapmap]
rs4802323	0.83[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes]
rs4802326	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4802327	0.90[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4804046	0.88[MEX][hapmap]
rs7256575	0.80[EUR][1000 genomes]
rs8104823	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8106900	0.88[MEX][hapmap]
rs931749	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs870218	CYP2S1	cis	cerebellum	SCAN
rs870218	C19orf33	cis	Heart Left Ventricle	GTEx
rs870218	APOC4	cis	cerebellum	SCAN
rs870218	C19orf33	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38756600-38772600	Weak transcription	Primary T cells from cord blood	blood
2	chr19:38756600-38772600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:38756800-38772600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr19:38756800-38774800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr19:38756800-38775000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:38756800-38778600	Weak transcription	Thymus	Thymus
7	chr19:38756800-38779600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:38758000-38774200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr19:38758400-38774400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:38759600-38783200	Weak transcription	Fetal Brain Male	brain
11	chr19:38761600-38773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:38764400-38771200	Weak transcription	Liver	Liver
13	chr19:38765800-38772400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:38765800-38794800	Weak transcription	Small Intestine	intestine
15	chr19:38767600-38772000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr19:38768800-38772600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:38769000-38771200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:38769000-38771200	Strong transcription	Fetal Intestine Small	intestine
19	chr19:38769200-38771400	Enhancers	Fetal Lung	lung
20	chr19:38769200-38772800	Weak transcription	Fetal Thymus	thymus
21	chr19:38769200-38773800	Weak transcription	Stomach Mucosa	stomach
22	chr19:38769200-38774400	Genic enhancers	HMEC	breast
23	chr19:38769200-38774800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr19:38769200-38778400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:38769200-38791200	Weak transcription	Fetal Kidney	kidney
26	chr19:38769400-38772800	Weak transcription	Ovary	ovary
27	chr19:38769400-38776000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:38769400-38779200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr19:38769600-38771800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:38769600-38775200	Weak transcription	NHDF-Ad	bronchial
32	chr19:38769600-38778400	Weak transcription	Brain Substantia Nigra	brain
33	chr19:38769800-38772600	Weak transcription	HSMMtube	muscle
34	chr19:38769800-38773000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:38769800-38775600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:38769800-38775800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:38769800-38778000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:38769800-38778200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:38769800-38778200	Weak transcription	Brain Hippocampus Middle	brain
40	chr19:38769800-38779000	Weak transcription	Brain Anterior Caudate	brain
41	chr19:38769800-38779000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:38769800-38779000	Weak transcription	HSMM	muscle
43	chr19:38769800-38779200	Weak transcription	Brain Angular Gyrus	brain
44	chr19:38769800-38780400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:38770000-38774000	Weak transcription	HUVEC	blood vessel
46	chr19:38770000-38780600	Weak transcription	Brain Germinal Matrix	brain
47	chr19:38770400-38771200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:38770400-38771400	Enhancers	Left Ventricle	heart
49	chr19:38770400-38771800	Enhancers	Fetal Heart	heart
50	chr19:38770400-38772000	Enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links