Variant report

Variant	rs4801170
Chromosome Location	chr19:57019430-57019431
allele	C/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	NRF1	chr19:57018621-57020372	SK-N-SH	brain:	n/a	chr19:57019014-57019028 chr19:57019208-57019219 chr19:57019011-57019025 chr19:57019016-57019025 chr19:57019210-57019219 chr19:57019208-57019222 chr19:57019014-57019025
2	CHD2	chr19:57018785-57019737	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr19:57018791-57019561	IMR90	lung:	n/a	chr19:57019188-57019198 chr19:57019273-57019287
4	TAF1	chr19:57019015-57019605	H1-neurons	neurons:	n/a	n/a
5	FOXP2	chr19:57018808-57019558	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr19:57019086-57019595	ECC-1	luminal epithelium:	n/a	n/a
7	SIX5	chr19:57019134-57019575	H1-hESC	embryonic stem cell:	n/a	chr19:57019405-57019419 chr19:57019407-57019416 chr19:57019409-57019418
8	MXI1	chr19:57018571-57020457	IMR90	lung:	n/a	chr19:57020209-57020218
9	MXI1	chr19:57018675-57019492	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr19:57018632-57019643	ECC-1	luminal epithelium:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
11	SIN3A	chr19:57018519-57020072	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:57018977-57019681	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr19:57018640-57020092	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr19:57018956-57019811	SK-N-MC	brain:	n/a	n/a
15	ZNF143	chr19:57018890-57019745	H1-hESC	embryonic stem cell:	n/a	chr19:57019091-57019101 chr19:57019407-57019425 chr19:57019407-57019416 chr19:57019409-57019418
16	REST	chr19:57018371-57020050	H1-neurons	neurons:	n/a	chr19:57018882-57018889
17	POLR2A	chr19:57018972-57019696	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr19:57018930-57019851	Gliobla	brain:	n/a	n/a
19	POLR2A	chr19:57019110-57019591	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr19:57018827-57019676	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr19:57019048-57020231	IMR90	lung:	n/a	n/a
22	MAX	chr19:57018659-57019690	SK-N-SH	brain:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
23	CREB1	chr19:57018823-57019608	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:57019138-57019707	ProgFib	skin:	n/a	n/a
25	MXI1	chr19:57018355-57020592	SK-N-SH	brain:	n/a	chr19:57020209-57020218
26	MAZ	chr19:57018669-57020086	IMR90	lung:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
27	POLR2A	chr19:57018736-57019515	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:57019006-57019599	HUVEC	blood vessel:	n/a	n/a
29	YY1	chr19:57019221-57019575	SK-N-SH_RA	brain:	n/a	n/a
30	MAX	chr19:57018555-57019580	SK-N-SH	brain:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
31	SP1	chr19:57018823-57019510	H1-hESC	embryonic stem cell:	n/a	chr19:57019450-57019462 chr19:57019171-57019182
32	MAX	chr19:57018569-57019503	ECC-1	luminal epithelium:	n/a	chr19:57019280-57019290 chr19:57018895-57018904
33	POLR2A	chr19:57018674-57020096	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ZNF471	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1029709	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10406304	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12979404	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2189699	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4801172	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73629994	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8101060	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8107062	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917406	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4801170	ZNF470	cis	multi-tissue	Pritchard
rs4801170	ZFP28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57018200-57019600	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr19:57018200-57019800	Active TSS	Brain Hippocampus Middle	brain
3	chr19:57018200-57019800	Active TSS	Fetal Lung	lung
4	chr19:57018200-57020200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:57018400-57019600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr19:57018400-57019800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:57018400-57019800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:57018400-57019800	Active TSS	Brain Angular Gyrus	brain
9	chr19:57018400-57019800	Active TSS	Brain Cingulate Gyrus	brain
10	chr19:57018400-57019800	Active TSS	Brain Substantia Nigra	brain
11	chr19:57018400-57019800	Active TSS	Colon Smooth Muscle	Colon
12	chr19:57018400-57019800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr19:57018400-57019800	Active TSS	Right Atrium	heart
14	chr19:57018400-57019800	Active TSS	HSMMtube	muscle
15	chr19:57018400-57019800	Active TSS	NHLF	lung
16	chr19:57018400-57020000	Active TSS	Psoas Muscle	Psoas
17	chr19:57018400-57020400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:57018400-57020400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr19:57018600-57019600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:57018600-57019600	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr19:57018600-57019600	Active TSS	Rectal Smooth Muscle	rectum
22	chr19:57018600-57019800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:57018600-57019800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:57018600-57019800	Active TSS	Brain Germinal Matrix	brain
25	chr19:57018600-57019800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:57018600-57019800	Active TSS	Fetal Brain Male	brain
27	chr19:57018600-57019800	Active TSS	Fetal Heart	heart
28	chr19:57018600-57019800	Active TSS	Fetal Kidney	kidney
29	chr19:57018600-57019800	Active TSS	Fetal Stomach	stomach
30	chr19:57018600-57019800	Active TSS	Ovary	ovary
31	chr19:57018600-57019800	Active TSS	Right Ventricle	heart
32	chr19:57018600-57019800	Active TSS	NHDF-Ad	bronchial
33	chr19:57018600-57020000	Active TSS	H9 Cell Line	embryonic stem cell
34	chr19:57018600-57020000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:57018600-57020000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:57018600-57020000	Active TSS	Fetal Intestine Large	intestine
37	chr19:57018600-57020000	ZNF genes & repeats	A549	lung
38	chr19:57018600-57020200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr19:57018600-57020200	Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:57018600-57020200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:57018600-57020200	Active TSS	Aorta	Aorta
42	chr19:57018600-57020200	Active TSS	Fetal Muscle Trunk	muscle
43	chr19:57018600-57020400	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr19:57018600-57020400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
45	chr19:57018600-57020400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
46	chr19:57018600-57020400	ZNF genes & repeats	Spleen	Spleen
47	chr19:57018800-57019600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr19:57018800-57019600	Active TSS	Primary B cells from cord blood	blood
49	chr19:57018800-57019600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr19:57018800-57019800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links