Variant report

Variant	rs9899509
Chromosome Location	chr17:38669819-38669820
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	ZNF263	chr17:38669367-38670943	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38640900..38643857-chr17:38669358..38670867,2	MCF-7	breast:
2	chr17:38643054..38644856-chr17:38668442..38670068,2	MCF-7	breast:
3	chr17:38661296..38663245-chr17:38668253..38670398,2	MCF-7	breast:
4	chr17:38648823..38651196-chr17:38668294..38669923,2	K562	blood:
5	chr17:38669573..38672204-chr17:38673213..38675996,3	K562	blood:

Variant related genes	Relation type
ENSG00000266088	TF binding region
ENSG00000266088	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1072070	0.87[EUR][1000 genomes]
rs11871009	1.00[EUR][1000 genomes]
rs16965857	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965864	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485796	1.00[EUR][1000 genomes]
rs3866675	1.00[EUR][1000 genomes]
rs56151683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7208120	1.00[EUR][1000 genomes]
rs7217539	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7222478	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8064741	1.00[EUR][1000 genomes]
rs8064890	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8065657	1.00[EUR][1000 genomes]
rs9894865	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909468	1.00[EUR][1000 genomes]
rs9910719	1.00[EUR][1000 genomes]
rs9915820	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38665800-38670200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr17:38666000-38670200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:38666200-38670000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:38666200-38670600	Enhancers	Placenta	Placenta
5	chr17:38666600-38670200	Enhancers	NHEK	skin
6	chr17:38666800-38670400	Weak transcription	Spleen	Spleen
7	chr17:38666800-38670600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr17:38666800-38671400	Weak transcription	Left Ventricle	heart
9	chr17:38666800-38674400	Weak transcription	Pancreas	Pancrea
10	chr17:38666800-38675000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:38666800-38677400	Weak transcription	Right Atrium	heart
12	chr17:38667000-38673000	Enhancers	A549	lung
13	chr17:38667400-38673000	Weak transcription	Esophagus	oesophagus
14	chr17:38668200-38671400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr17:38668200-38677400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:38668400-38671400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:38668400-38680600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:38668600-38672800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr17:38668600-38675200	Weak transcription	Gastric	stomach
20	chr17:38668800-38671400	Weak transcription	Lung	lung
21	chr17:38668800-38672600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:38668800-38672600	Weak transcription	Osteobl	bone
23	chr17:38668800-38674600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr17:38669000-38670000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:38669000-38670400	Enhancers	HepG2	liver
26	chr17:38669000-38670600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:38669000-38670800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:38669000-38671200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:38669000-38671200	Weak transcription	HMEC	breast
30	chr17:38669000-38671400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr17:38669000-38671400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr17:38669000-38671600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr17:38669000-38672200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:38669000-38672800	Weak transcription	NHLF	lung
35	chr17:38669000-38673000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr17:38669400-38670000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:38669400-38672800	Enhancers	Hela-S3	cervix
38	chr17:38669600-38670200	Enhancers	K562	blood
39	chr17:38669600-38670200	Bivalent Enhancer	NH-A	brain
40	chr17:38669600-38670800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:38669800-38670000	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr17:38669800-38670000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
43	chr17:38669800-38670000	Enhancers	Psoas Muscle	Psoas
44	chr17:38669800-38670200	Enhancers	HSMMtube	muscle
45	chr17:38669800-38672800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:38669800-38672800	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links