Variant report

Variant	rs17680410
Chromosome Location	chr17:38557568-38557569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38557353-38558258	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr17:38554779-38557569	K562	blood:	n/a	n/a
3	POLR2A	chr17:38557216-38558006	HepG2	liver:	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	chr17:38556973..38559304-chr17:38571914..38574386,4	K562	blood:
3	chr17:38538967..38540693-chr17:38555922..38558786,2	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: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10305288	1.00[AFR][1000 genomes]
rs10305296	1.00[AFR][1000 genomes]
rs10305303	1.00[AFR][1000 genomes]
rs10512482	0.92[EUR][1000 genomes]
rs11540720	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11867902	1.00[CEU][hapmap]
rs12103533	0.92[EUR][1000 genomes]
rs15685	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965660	0.92[EUR][1000 genomes]
rs16965669	0.92[EUR][1000 genomes]
rs16965734	0.92[EUR][1000 genomes]
rs16965736	0.92[EUR][1000 genomes]
rs16965748	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16965774	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16965778	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17557495	1.00[AFR][1000 genomes]
rs17616672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17618397	1.00[AFR][1000 genomes]
rs17678817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679038	1.00[AFR][1000 genomes]
rs17679086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679361	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17680704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2012667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229773	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362320	0.92[EUR][1000 genomes]
rs28362321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33998939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34270904	0.92[EUR][1000 genomes]
rs34300454	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs35783632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35898909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41283417	0.92[EUR][1000 genomes]
rs41283423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134998	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135019	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135027	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135030	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45612441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214783	0.85[EUR][1000 genomes]
rs72819623	1.00[AFR][1000 genomes]
rs72819624	1.00[AFR][1000 genomes]
rs72819628	1.00[AFR][1000 genomes]
rs72819630	1.00[AFR][1000 genomes]
rs72819632	1.00[AFR][1000 genomes]
rs72819633	1.00[AFR][1000 genomes]
rs72819651	1.00[AFR][1000 genomes]
rs8067519	0.92[EUR][1000 genomes]
rs8071687	0.92[EUR][1000 genomes]
rs9889905	0.92[EUR][1000 genomes]
rs9891944	1.00[EUR][1000 genomes]
rs9894364	0.92[EUR][1000 genomes]
rs9894807	0.92[EUR][1000 genomes]
rs9898500	0.92[EUR][1000 genomes]
rs9903293	0.92[EUR][1000 genomes]
rs9909777	0.92[EUR][1000 genomes]
rs9909811	0.92[EUR][1000 genomes]
rs9910373	0.92[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

No data

Chromatin state (count:80 , 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	chr17:38538400-38559200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:38539400-38565800	Weak transcription	Placenta	Placenta
5	chr17:38540200-38571400	Strong transcription	Fetal Thymus	thymus
6	chr17:38541800-38559000	Strong transcription	A549	lung
7	chr17:38542200-38571600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:38542400-38560400	Strong transcription	Dnd41	blood
9	chr17:38542600-38566000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr17:38542600-38566400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:38542600-38571800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:38543000-38566000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:38543200-38559000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:38543200-38571000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:38543400-38571000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:38543400-38571400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:38543400-38571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:38543800-38566000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr17:38543800-38566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr17:38543800-38566400	Weak transcription	Fetal Heart	heart
21	chr17:38544000-38561200	Strong transcription	Hela-S3	cervix
22	chr17:38544000-38566600	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr17:38544000-38566800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:38544000-38569800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:38544000-38570200	Strong transcription	HepG2	liver
26	chr17:38544000-38571800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:38544200-38561400	Strong transcription	Osteobl	bone
28	chr17:38544200-38567000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:38544400-38566600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr17:38544400-38573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:38545200-38573200	Weak transcription	Gastric	stomach
32	chr17:38546000-38573600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:38546400-38572200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr17:38546400-38572800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:38546400-38573200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr17:38547800-38559000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr17:38547800-38565200	Weak transcription	Esophagus	oesophagus
38	chr17:38548200-38572000	Weak transcription	Brain Germinal Matrix	brain
39	chr17:38548400-38572800	Weak transcription	Primary B cells from cord blood	blood
40	chr17:38549800-38573000	Weak transcription	Fetal Intestine Large	intestine
41	chr17:38550400-38558000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:38551000-38573000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:38551600-38560600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:38552200-38564000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr17:38552200-38573400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:38553400-38557600	Weak transcription	Thymus	Thymus
47	chr17:38553400-38560600	Strong transcription	NH-A	brain
48	chr17:38553400-38561200	Weak transcription	Fetal Stomach	stomach
49	chr17:38553600-38562200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr17:38554000-38560800	Strong transcription	NHEK	skin

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