Variant report

Variant	rs486466
Chromosome Location	chr19:37346984-37346985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37340586..37343118-chr19:37344104..37346997,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251247	Chromatin interaction
ENSG00000197863	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10401212	0.87[CHB][hapmap]
rs10403100	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10403306	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10403906	0.86[ASN][1000 genomes]
rs10409144	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10411509	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10418176	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10418453	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1423048	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34201634	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3955478	0.88[CHB][hapmap]
rs477725	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs477942	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478272	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491898	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs493482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs497144	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs502110	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503956	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503959	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs505896	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs506463	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs546693	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553981	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs555023	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559008	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs560085	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs566432	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571074	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs577093	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs578699	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs579445	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs580168	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs581194	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7256044	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73611677	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs826276	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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	73 gene(s)	inside rSNPs	diseases
6	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3517005	chr19:37193712-37364110	Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	esv3517004	chr19:37193762-37363960	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv3517006	chr19:37193762-37363960	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv1060155	chr19:37274915-37458788	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv544000	chr19:37274915-37458788	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
15	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
17	nsv911651	chr19:37300554-37428465	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	esv3354270	chr19:37309161-37364929	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
20	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
21	nsv458569	chr19:37331614-37412887	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv579462	chr19:37331614-37412887	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs486466	ZNF420	cis	Lymphoblastoid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37342800-37347400	Weak transcription	Psoas Muscle	Psoas
2	chr19:37342800-37348400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:37342800-37348600	Weak transcription	Esophagus	oesophagus
4	chr19:37342800-37348800	Weak transcription	Brain Angular Gyrus	brain
5	chr19:37342800-37353800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:37342800-37353800	Weak transcription	HUVEC	blood vessel
7	chr19:37342800-37355000	Weak transcription	Osteobl	bone
8	chr19:37342800-37356800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:37343000-37347000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:37343000-37347400	Weak transcription	Pancreas	Pancrea
11	chr19:37343000-37351400	Weak transcription	Right Ventricle	heart
12	chr19:37343400-37352600	ZNF genes & repeats	Fetal Brain Female	brain
13	chr19:37343400-37356000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:37343600-37358600	ZNF genes & repeats	Brain Germinal Matrix	brain
15	chr19:37343600-37359000	ZNF genes & repeats	Fetal Lung	lung
16	chr19:37344000-37350000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:37344200-37350400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:37344400-37347400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:37344400-37347800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
20	chr19:37344400-37349200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
21	chr19:37344400-37349800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:37344400-37356000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr19:37344400-37369400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:37344400-37371600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:37344400-37406400	ZNF genes & repeats	Liver	Liver
26	chr19:37344600-37347400	Strong transcription	Ovary	ovary
27	chr19:37344600-37347800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
28	chr19:37344600-37348200	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr19:37344600-37348800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr19:37344600-37352200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:37344600-37371600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr19:37345000-37347600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:37345000-37356000	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr19:37345200-37347000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:37345200-37347000	ZNF genes & repeats	Thymus	Thymus
36	chr19:37345200-37347800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:37345200-37349200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr19:37345200-37353800	Weak transcription	Fetal Heart	heart
39	chr19:37345400-37349600	ZNF genes & repeats	Fetal Stomach	stomach
40	chr19:37345400-37353600	Weak transcription	HSMMtube	muscle
41	chr19:37345600-37347400	Weak transcription	Left Ventricle	heart
42	chr19:37345600-37349000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:37345600-37350800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:37345800-37347000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:37345800-37347800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr19:37346000-37350200	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:37346200-37347000	ZNF genes & repeats	Fetal Thymus	thymus
48	chr19:37346200-37349800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:37346200-37350000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
50	chr19:37346400-37347000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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