Variant report

Variant	rs2304123
Chromosome Location	chr19:56887208-56887209
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	chr19:56886550..56889123-chr19:56903257..56905976,3	K562	blood:

Variant related genes	Relation type
ENSG00000267454	Chromatin interaction
ENSG00000018869	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1017102	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10401898	0.81[ASN][1000 genomes]
rs10405914	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs10413341	0.83[ASN][1000 genomes]
rs10418348	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10419074	0.82[ASW][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs10419213	0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs12608563	0.95[ASN][1000 genomes]
rs12610246	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12610899	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12978696	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12981331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12983342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12983411	0.81[ASN][1000 genomes]
rs2288856	0.89[CHB][hapmap];0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs2304125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2304127	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]
rs4334405	0.86[ASN][1000 genomes]
rs4801717	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs8111942	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2304123	ZNF134	cis	cerebellum	SCAN
rs2304123	ZNF134	cis	parietal	SCAN
rs2304123	ZNF772	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56880600-56890600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:56880600-56890800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:56880600-56891200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:56880600-56891400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:56880800-56888400	Weak transcription	Stomach Mucosa	stomach
6	chr19:56880800-56890600	ZNF genes & repeats	Primary B cells from cord blood	blood
7	chr19:56880800-56890800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
8	chr19:56881000-56890800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:56881000-56891000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:56881200-56892200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:56881200-56904000	ZNF genes & repeats	Liver	Liver
12	chr19:56881400-56890600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:56881400-56893000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:56881800-56890800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:56881800-56890800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:56882000-56887600	ZNF genes & repeats	Aorta	Aorta
17	chr19:56882000-56887800	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr19:56882000-56888200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:56882000-56890200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:56882000-56890600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:56882000-56890800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:56882200-56888000	Strong transcription	Fetal Brain Female	brain
23	chr19:56882200-56890200	Strong transcription	Brain Germinal Matrix	brain
24	chr19:56882200-56891200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:56882400-56889800	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:56882600-56888200	Strong transcription	Brain Hippocampus Middle	brain
27	chr19:56882800-56887600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:56882800-56888200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:56883200-56888800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:56883200-56889200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
31	chr19:56883200-56889200	ZNF genes & repeats	A549	lung
32	chr19:56883200-56889400	Strong transcription	Fetal Thymus	thymus
33	chr19:56883200-56889400	ZNF genes & repeats	NHEK	skin
34	chr19:56883400-56888400	Strong transcription	Left Ventricle	heart
35	chr19:56883400-56888400	Strong transcription	Rectal Smooth Muscle	rectum
36	chr19:56883400-56889200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr19:56883400-56889400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
38	chr19:56883400-56889600	ZNF genes & repeats	Fetal Lung	lung
39	chr19:56883400-56890200	Strong transcription	Fetal Brain Male	brain
40	chr19:56883400-56890200	ZNF genes & repeats	Ovary	ovary
41	chr19:56883400-56890400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
42	chr19:56883400-56890600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:56883400-56890800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
44	chr19:56883400-56891000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:56883400-56891200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:56883600-56890000	Strong transcription	Brain Anterior Caudate	brain
47	chr19:56883600-56890600	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr19:56883800-56887800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:56883800-56888200	Strong transcription	Brain Angular Gyrus	brain
50	chr19:56883800-56888400	Strong transcription	Brain Cingulate Gyrus	brain

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