Variant report

Variant	rs17660487
Chromosome Location	chr19:52084234-52084235
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	POLR2A	chr19:52083599-52085259	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52073774..52076492-chr19:52083212..52084974,2	K562	blood:

Variant related genes	Relation type
ZNF175	TF binding region
ENSG00000105497	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1063973	0.87[ASN][1000 genomes]
rs12973066	1.00[ASN][1000 genomes]
rs12973225	1.00[ASN][1000 genomes]
rs35589997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35936222	1.00[ASN][1000 genomes]
rs3752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45541134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57351606	0.87[ASN][1000 genomes]
rs58301181	0.87[ASN][1000 genomes]
rs59191415	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67770878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17660487	SBK2	cis	cerebellum	SCAN
rs17660487	ZNF542	cis	cerebellum	SCAN
rs17660487	ZNF671	cis	parietal	SCAN
rs17660487	ZSCAN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52075400-52084600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:52075400-52087400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:52075400-52090200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:52075600-52084400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:52075600-52084400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:52075600-52084600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:52075600-52084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:52075600-52084600	Weak transcription	Colonic Mucosa	Colon
9	chr19:52075600-52084800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:52075600-52084800	Weak transcription	Fetal Kidney	kidney
11	chr19:52075600-52089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:52075800-52085000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr19:52075800-52090000	Weak transcription	Stomach Mucosa	stomach
14	chr19:52075800-52096800	Weak transcription	HepG2	liver
15	chr19:52076000-52084800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:52076200-52084600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr19:52076200-52084800	Weak transcription	Fetal Heart	heart
18	chr19:52076200-52088200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr19:52076400-52086800	Strong transcription	Primary T cells from cord blood	blood
20	chr19:52076400-52087000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:52076400-52088800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:52076800-52084600	Weak transcription	Esophagus	oesophagus
23	chr19:52076800-52087400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:52076800-52089400	Weak transcription	HMEC	breast
25	chr19:52077000-52084400	Weak transcription	Psoas Muscle	Psoas
26	chr19:52077000-52084800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:52077000-52088800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:52077000-52089600	Weak transcription	Small Intestine	intestine
29	chr19:52077000-52097000	Weak transcription	Hela-S3	cervix
30	chr19:52077200-52084600	Weak transcription	Right Ventricle	heart
31	chr19:52077200-52089400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:52077400-52084600	Weak transcription	NHEK	skin
33	chr19:52077600-52087400	Strong transcription	Osteobl	bone
34	chr19:52078000-52084600	Weak transcription	Brain Angular Gyrus	brain
35	chr19:52078200-52084600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr19:52078200-52089600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr19:52078400-52087400	Strong transcription	Dnd41	blood
38	chr19:52078600-52084600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:52078600-52088200	Weak transcription	Fetal Intestine Small	intestine
40	chr19:52078800-52087000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:52079000-52089200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:52079200-52084800	Weak transcription	NH-A	brain
43	chr19:52079200-52087600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:52080000-52084600	Weak transcription	NHLF	lung
45	chr19:52080200-52084600	Weak transcription	Gastric	stomach
46	chr19:52080200-52084600	Weak transcription	Pancreas	Pancrea
47	chr19:52080400-52084600	Weak transcription	Brain Substantia Nigra	brain
48	chr19:52080600-52084400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr19:52080600-52084800	Weak transcription	Fetal Brain Male	brain
50	chr19:52080600-52086400	Weak transcription	NHDF-Ad	bronchial

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