Variant report

Variant	rs471692
Chromosome Location	chr17:38556770-38556771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38554779-38557569	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38555801..38558775-chr17:38573613..38575246,2	MCF-7	breast:
2	chr17:38538967..38540693-chr17:38555922..38558786,2	K562	blood:
3	chr17:38556023..38556886-chr17:38689269..38690202,2	K562	blood:
4	chr17:38544588..38548116-chr17:38554882..38558246,4	K562	blood:
5	chr17:38545957..38547711-chr17:38556423..38558045,2	K562	blood:
6	chr17:38556420..38558827-chr17:38559237..38561235,2	MCF-7	breast:

No data

Variant related genes	Relation type
TOP2A	TF binding region
ENSG00000131747	Chromatin interaction
ENSG00000222881	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1530363	0.81[CEU][hapmap];0.98[GIH][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs1662574	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16965783	0.93[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2586112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715556	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2715557	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473198	1.00[ASW][hapmap];0.93[CEU][hapmap];0.98[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs474510	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs477220	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs495511	0.83[EUR][1000 genomes]
rs505633	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506728	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507564	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs510336	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs517047	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs525217	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs525812	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs528045	0.82[EUR][1000 genomes]
rs532299	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs552857	0.86[EUR][1000 genomes]
rs557498	0.86[EUR][1000 genomes]
rs558068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62066565	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs471692	KRT33B	cis	parietal	SCAN
rs471692	MYO19	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38536800-38562000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr17:38537200-38558600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:38538200-38557400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:38538400-38559200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:38539400-38565800	Weak transcription	Placenta	Placenta
6	chr17:38540200-38571400	Strong transcription	Fetal Thymus	thymus
7	chr17:38541800-38559000	Strong transcription	A549	lung
8	chr17:38542000-38556800	Weak transcription	Fetal Lung	lung
9	chr17:38542200-38571600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:38542400-38560400	Strong transcription	Dnd41	blood
11	chr17:38542600-38566000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:38542600-38566400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:38542600-38571800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr17:38543000-38557000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr17:38543000-38566000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr17:38543200-38559000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:38543200-38571000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:38543400-38571000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr17:38543400-38571400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:38543400-38571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:38543800-38566000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr17:38543800-38566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr17:38543800-38566400	Weak transcription	Fetal Heart	heart
24	chr17:38544000-38561200	Strong transcription	Hela-S3	cervix
25	chr17:38544000-38566600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr17:38544000-38566800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr17:38544000-38569800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:38544000-38570200	Strong transcription	HepG2	liver
29	chr17:38544000-38571800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr17:38544200-38561400	Strong transcription	Osteobl	bone
31	chr17:38544200-38567000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:38544400-38566600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr17:38544400-38573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:38545200-38573200	Weak transcription	Gastric	stomach
35	chr17:38546000-38573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:38546400-38572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr17:38546400-38572800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:38546400-38573200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr17:38547800-38559000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:38547800-38565200	Weak transcription	Esophagus	oesophagus
41	chr17:38548200-38572000	Weak transcription	Brain Germinal Matrix	brain
42	chr17:38548400-38556800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr17:38548400-38572800	Weak transcription	Primary B cells from cord blood	blood
44	chr17:38549400-38557200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr17:38549800-38573000	Weak transcription	Fetal Intestine Large	intestine
46	chr17:38550400-38558000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:38551000-38573000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr17:38551600-38560600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr17:38552200-38564000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr17:38552200-38573400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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