Variant report

Variant	rs2288862
Chromosome Location	chr19:56918574-56918575
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	chr19:56914950..56917627-chr19:56917967..56921707,4	K562	blood:

Variant related genes	Relation type
ENSG00000198440	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11084447	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11084448	0.82[CHB][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12709959	0.85[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12979827	0.87[ASN][1000 genomes]
rs12984960	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2215410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288860	0.82[JPT][hapmap]
rs2288863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28815239	0.90[ASN][1000 genomes]
rs4239475	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4801159	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801160	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801161	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801316	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4801318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801720	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs62121591	0.93[ASN][1000 genomes]
rs62121592	0.90[ASN][1000 genomes]
rs62121594	0.90[ASN][1000 genomes]
rs62121597	0.84[ASN][1000 genomes]
rs6509995	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7246353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7253851	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113270	0.85[CHB][hapmap];1.00[JPT][hapmap]

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	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv544096	chr19:56905651-56933455	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	esv3373403	chr19:56913940-56918638	Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2288862	ZNF324	cis	cerebellum	SCAN
rs2288862	ZNF324	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56915800-56924200	ZNF genes & repeats	Fetal Brain Male	brain
2	chr19:56915800-56927000	ZNF genes & repeats	HSMM	muscle
3	chr19:56916000-56938600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:56916200-56919000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:56916200-56920200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:56916400-56918600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:56916400-56918600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:56916400-56920400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
9	chr19:56916400-56926200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:56916400-56927000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
11	chr19:56916400-56929800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr19:56916400-56936600	ZNF genes & repeats	Brain Germinal Matrix	brain
13	chr19:56916400-56956000	ZNF genes & repeats	Liver	Liver
14	chr19:56916600-56920000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:56916600-56920200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:56916600-56935600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:56916600-56956000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:56916800-56918600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:56916800-56918600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr19:56916800-56918600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:56916800-56918600	Weak transcription	Brain Substantia Nigra	brain
22	chr19:56916800-56918600	Weak transcription	NHEK	skin
23	chr19:56916800-56918800	Weak transcription	Fetal Thymus	thymus
24	chr19:56916800-56919600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:56916800-56920000	Weak transcription	Pancreas	Pancrea
26	chr19:56916800-56921800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:56916800-56936200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:56916800-56936200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:56917000-56918600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:56917000-56918800	Weak transcription	Right Ventricle	heart
31	chr19:56917000-56919000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:56917000-56919200	ZNF genes & repeats	Fetal Stomach	stomach
33	chr19:56917000-56920400	Strong transcription	Brain Angular Gyrus	brain
34	chr19:56917000-56926000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:56917000-56927200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr19:56917000-56931000	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr19:56917000-56931200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:56917000-56937000	ZNF genes & repeats	Fetal Lung	lung
39	chr19:56917000-56938800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:56917000-56940000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr19:56917200-56918600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:56917200-56929800	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr19:56917200-56935800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:56917200-56936600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr19:56917200-56936600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
46	chr19:56917200-56937600	ZNF genes & repeats	Fetal Brain Female	brain
47	chr19:56917400-56919000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:56917400-56924400	Weak transcription	K562	blood
49	chr19:56917400-56944800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:56917600-56918800	Weak transcription	Gastric	stomach

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