Variant report

Variant	rs2286423
Chromosome Location	chr19:57050820-57050821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr19:57049495-57051243	IMR90	lung:	n/a	n/a
2	TCF12	chr19:57050229-57050992	A549	lung:	n/a	n/a
3	SIN3A	chr19:57050336-57050920	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr19:57050203-57050976	A549	lung:	n/a	n/a
5	REST	chr19:57049096-57051000	H1-neurons	neurons:	n/a	chr19:57049698-57049706 chr19:57049912-57049925
6	POLR2A	chr19:57050194-57050828	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000267421	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10404464	0.80[EUR][1000 genomes]
rs10406513	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10406535	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10406985	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10408108	0.81[EUR][1000 genomes]
rs10414817	0.81[EUR][1000 genomes]
rs10415223	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416884	0.91[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417966	0.82[EUR][1000 genomes]
rs10419553	0.81[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10419939	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422306	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984487	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17144	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17273442	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2058132	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189698	0.81[EUR][1000 genomes]
rs35780595	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752176	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106523	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8106788	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958338	0.89[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MKK][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs960995	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs993510	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking 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	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription 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	14 gene(s)	inside rSNPs	diseases
12	nsv912519	chr19:57020754-57065189	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
13	nsv1062806	chr19:57050734-57191914	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2286423	ZNF547	cis	parietal	SCAN
rs2286423	ZNF471	trans	cerebellum	SCAN
rs2286423	ZNF837	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57047400-57077800	ZNF genes & repeats	Liver	Liver
2	chr19:57048800-57051200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr19:57048800-57051400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr19:57048800-57051600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:57048800-57053000	ZNF genes & repeats	Placenta	Placenta
6	chr19:57048800-57053000	ZNF genes & repeats	HSMM	muscle
7	chr19:57048800-57053800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:57049000-57051400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr19:57049200-57051000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:57049200-57051000	Active TSS	Fetal Kidney	kidney
11	chr19:57049200-57051200	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr19:57049200-57051200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:57049200-57051400	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr19:57049400-57051000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr19:57049400-57051000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:57049400-57051000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:57049400-57051000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:57049400-57051200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr19:57049400-57051200	Active TSS	Small Intestine	intestine
20	chr19:57049400-57051400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr19:57049600-57051000	Active TSS	Brain Substantia Nigra	brain
22	chr19:57049600-57051200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:57049600-57051200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr19:57049600-57051200	Active TSS	Primary T cells from cord blood	blood
25	chr19:57049600-57051200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:57049600-57051200	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr19:57049600-57051400	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr19:57049600-57051400	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr19:57049600-57051400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:57049600-57051400	Active TSS	HSMMtube	muscle
31	chr19:57049600-57052000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr19:57049800-57051000	Active TSS	NHEK	skin
33	chr19:57049800-57051200	Active TSS	Fetal Muscle Trunk	muscle
34	chr19:57050000-57051200	Active TSS	HMEC	breast
35	chr19:57050400-57051000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr19:57050400-57051000	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr19:57050400-57051000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr19:57050400-57051000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:57050400-57051000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr19:57050400-57051000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr19:57050400-57051000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr19:57050400-57051000	Flanking Active TSS	Colonic Mucosa	Colon
43	chr19:57050400-57051000	Flanking Active TSS	Pancreas	Pancrea
44	chr19:57050400-57051000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
45	chr19:57050400-57051000	Flanking Active TSS	Dnd41	blood
46	chr19:57050400-57051200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:57050400-57051200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:57050400-57051200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr19:57050400-57051400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:57050600-57051000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links