Variant report

Variant	rs56246998
Chromosome Location	chr19:36967032-36967033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36965657..36967855-chr19:36968852..36972035,4	K562	blood:
2	chr19:36965657..36967339-chr19:36969186..36972035,2	K562	blood:
3	chr19:36966764..36969281-chr19:36976956..36980463,3	K562	blood:
4	chr19:36966894..36968985-chr19:36971010..36973941,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186017	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs17707014	0.85[AMR][1000 genomes]
rs17707021	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2891868	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514798	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4806328	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806333	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs55743839	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801623	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs55830504	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs55880628	0.87[AMR][1000 genomes]
rs55933007	0.90[AMR][1000 genomes]
rs56054915	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075402	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183102	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510549	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249099	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259057	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032465	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032484	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73032489	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73032502	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73034109	0.90[AMR][1000 genomes]
rs73034142	0.83[AMR][1000 genomes]
rs73049817	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73049826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73049844	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73049851	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73049853	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100340	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102097	0.87[AMR][1000 genomes]
rs8103168	0.87[ASN][1000 genomes]
rs8103917	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104087	0.87[ASN][1000 genomes]
rs8104893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105973	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8110140	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised 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	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
6	nsv1067364	chr19:36921204-36985874	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56246998	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36936400-36978400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:36941000-36979000	Weak transcription	Hela-S3	cervix
3	chr19:36944800-36969600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr19:36945800-36979000	Weak transcription	Fetal Heart	heart
5	chr19:36947600-36977400	ZNF genes & repeats	Liver	Liver
6	chr19:36953200-36967600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:36953200-36967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:36953400-36967600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:36954000-36972200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:36954400-36967800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:36955600-36967200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr19:36957200-36979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:36957400-36979400	Weak transcription	NH-A	brain
14	chr19:36958200-36967600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:36958800-36971200	ZNF genes & repeats	A549	lung
16	chr19:36959600-36967200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr19:36960400-36979600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:36962600-36968200	Strong transcription	Brain Germinal Matrix	brain
19	chr19:36963200-36967800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:36963400-36979200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:36963800-36969400	Weak transcription	Spleen	Spleen
22	chr19:36964000-36970600	Weak transcription	NHDF-Ad	bronchial
23	chr19:36964000-36975000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:36964000-36979800	Weak transcription	Esophagus	oesophagus
25	chr19:36964200-36971200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr19:36964200-36978200	Weak transcription	Brain Angular Gyrus	brain
27	chr19:36964200-36979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr19:36964200-36979000	Weak transcription	Osteobl	bone
29	chr19:36964200-36979200	Weak transcription	Stomach Mucosa	stomach
30	chr19:36964200-36979400	Weak transcription	Brain Anterior Caudate	brain
31	chr19:36964200-36979600	Weak transcription	Placenta	Placenta
32	chr19:36964200-36979600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr19:36964400-36968200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:36964400-36970600	Weak transcription	Thymus	Thymus
35	chr19:36964400-36973400	Weak transcription	HepG2	liver
36	chr19:36964400-36974000	Weak transcription	Brain Substantia Nigra	brain
37	chr19:36964400-36978800	Weak transcription	K562	blood
38	chr19:36964400-36979000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:36964600-36969000	Weak transcription	Fetal Lung	lung
40	chr19:36964600-36973400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:36964600-36979200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr19:36964600-36979400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr19:36964800-36967400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:36964800-36974400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:36964800-36979600	Weak transcription	Fetal Kidney	kidney
46	chr19:36965000-36967400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr19:36965200-36968400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr19:36965200-36973200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:36965400-36967600	Weak transcription	Primary B cells from cord blood	blood
50	chr19:36965400-36967600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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