Variant report

Variant	rs4985966
Chromosome Location	chr17:20942333-20942334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20934273..20942906-chr17:20943761..20949798,22	MCF-7	breast:
2	chr17:20929697..20932170-chr17:20941265..20943012,2	MCF-7	breast:
3	chr17:20942123..20943624-chr17:21186907..21188806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction
ENSG00000034152	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1045162	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1127814	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12051606	0.90[AMR][1000 genomes]
rs12600703	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12601292	0.86[AMR][1000 genomes]
rs12602058	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12946114	0.85[ASN][1000 genomes]
rs1542552	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17770614	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054464	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2127095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291034	0.85[ASN][1000 genomes]
rs2364326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2886105	0.86[AMR][1000 genomes]
rs4445951	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4985811	0.90[AMR][1000 genomes]
rs4985814	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985815	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4985816	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985963	0.83[ASN][1000 genomes]
rs4985967	0.81[ASN][1000 genomes]
rs4985968	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985970	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985971	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56323013	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58235085	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59543297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59713572	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs719093	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7209129	0.82[ASN][1000 genomes]
rs880653	0.86[AMR][1000 genomes]
rs899337	0.87[AMR][1000 genomes]
rs899340	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv827918	chr17:20941127-20951156	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4985966	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs4985966	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs4985966	RP11-344E13.3	cis	Stomach	GTEx
rs4985966	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs4985966	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs4985966	RP11-344E13.3	cis	Artery Tibial	GTEx
rs4985966	RP11-344E13.3	cis	Whole Blood	GTEx
rs4985966	RP11-344E13.3	cis	lung	GTEx
rs4985966	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs4985966	RP11-344E13.3	cis	Thyroid	GTEx
rs4985966	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs4985966	RP11-344E13.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:20934000-20942800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:20934000-20943200	Weak transcription	Esophagus	oesophagus
4	chr17:20935200-20943800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr17:20936800-20943800	Enhancers	Liver	Liver
6	chr17:20938200-20943600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr17:20938400-20943200	Weak transcription	Lung	lung
8	chr17:20938400-20944000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:20939000-20943200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr17:20939200-20942800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:20939400-20942400	Enhancers	Brain Germinal Matrix	brain
12	chr17:20939400-20943200	Enhancers	Right Atrium	heart
13	chr17:20939600-20942400	Genic enhancers	K562	blood
14	chr17:20940200-20942600	Enhancers	Pancreas	Pancrea
15	chr17:20940200-20943000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:20940200-20943600	Genic enhancers	Fetal Thymus	thymus
17	chr17:20940400-20943200	Enhancers	Psoas Muscle	Psoas
18	chr17:20940800-20942800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr17:20940800-20943000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr17:20940800-20943200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:20940800-20943200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:20941000-20942600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr17:20941000-20942800	Weak transcription	Stomach Mucosa	stomach
24	chr17:20941000-20942800	Genic enhancers	Dnd41	blood
25	chr17:20941000-20942800	Weak transcription	HMEC	breast
26	chr17:20941000-20943000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr17:20941000-20943200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr17:20941000-20943200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr17:20941000-20943200	Strong transcription	Fetal Intestine Small	intestine
30	chr17:20941000-20943200	Strong transcription	Fetal Stomach	stomach
31	chr17:20941000-20943200	Weak transcription	Gastric	stomach
32	chr17:20941000-20943600	Weak transcription	Right Ventricle	heart
33	chr17:20941000-20944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:20941000-20944000	Weak transcription	Fetal Intestine Large	intestine
35	chr17:20941200-20942600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr17:20941200-20942800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:20941200-20942800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:20941200-20942800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr17:20941200-20942800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr17:20941200-20942800	Weak transcription	Hela-S3	cervix
41	chr17:20941200-20942800	Weak transcription	NHLF	lung
42	chr17:20941200-20943000	Weak transcription	Brain Angular Gyrus	brain
43	chr17:20941200-20943000	Weak transcription	Fetal Brain Female	brain
44	chr17:20941200-20943000	Genic enhancers	Osteobl	bone
45	chr17:20941200-20943200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:20941200-20943200	Enhancers	HUVEC	blood vessel
47	chr17:20941200-20943400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:20941200-20943600	Weak transcription	HSMMtube	muscle
49	chr17:20941400-20942600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:20941400-20942600	Weak transcription	Fetal Heart	heart

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