Variant report

Variant	rs2364326
Chromosome Location	chr17:20939464-20939465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20930469..20933824-chr17:20936944..20940043,3	MCF-7	breast:
2	chr17:20932232..20934940-chr17:20938795..20941578,2	MCF-7	breast:
3	chr17:20934273..20942906-chr17:20943761..20949798,22	MCF-7	breast:
4	chr17:20936833..20939628-chr17:20939684..20941380,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124422	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1045162	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1127814	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12051606	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12600703	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12601292	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12602058	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12943067	0.83[ASN][1000 genomes]
rs12946114	0.90[ASN][1000 genomes]
rs1542552	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17770614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2054464	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2127095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291034	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2886105	0.86[AMR][1000 genomes]
rs4445951	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985811	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4985814	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985815	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985816	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4985959	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4985963	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4985966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985967	0.86[ASN][1000 genomes]
rs4985968	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985970	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985971	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56323013	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58235085	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59543297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59713572	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6587111	0.85[ASN][1000 genomes]
rs6587114	0.83[ASN][1000 genomes]
rs6618	0.84[ASN][1000 genomes]
rs719093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209129	0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7216921	0.82[ASN][1000 genomes]
rs880653	0.86[AMR][1000 genomes]
rs899337	0.87[AMR][1000 genomes]
rs899340	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9911289	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2364326	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs2364326	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs2364326	RP11-344E13.3	cis	Whole Blood	GTEx
rs2364326	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs2364326	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs2364326	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2364326	RP11-344E13.3	cis	Artery Tibial	GTEx
rs2364326	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs2364326	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs2364326	RP11-344E13.3	cis	Stomach	GTEx
rs2364326	RP11-344E13.3	cis	lung	GTEx
rs2364326	RP11-344E13.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20903400-20940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:20923000-20943800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:20931800-20940200	Enhancers	Brain Cingulate Gyrus	brain
4	chr17:20932200-20941400	Genic enhancers	A549	lung
5	chr17:20932600-20940400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:20932800-20941800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:20934000-20942800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:20934000-20943200	Weak transcription	Esophagus	oesophagus
9	chr17:20934600-20940000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr17:20935000-20940600	Enhancers	Left Ventricle	heart
11	chr17:20935000-20941000	Enhancers	Right Ventricle	heart
12	chr17:20935200-20943800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr17:20935600-20940000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr17:20935600-20940200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:20935600-20942200	Enhancers	Fetal Brain Male	brain
16	chr17:20935800-20940600	Enhancers	Fetal Heart	heart
17	chr17:20936000-20939600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:20936200-20941600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:20936400-20939600	Enhancers	K562	blood
20	chr17:20936400-20939800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr17:20936400-20940800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr17:20936600-20941000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr17:20936600-20941200	Genic enhancers	HUVEC	blood vessel
24	chr17:20936800-20939800	Enhancers	HepG2	liver
25	chr17:20936800-20941800	Genic enhancers	NHEK	skin
26	chr17:20936800-20942000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:20936800-20943800	Enhancers	Liver	Liver
28	chr17:20937000-20939600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr17:20937000-20940200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr17:20937400-20939800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:20937400-20941200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:20937400-20941200	Enhancers	Colonic Mucosa	Colon
33	chr17:20937600-20939600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr17:20937600-20941400	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr17:20937600-20942000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
36	chr17:20937800-20940000	Enhancers	Fetal Kidney	kidney
37	chr17:20937800-20940200	Enhancers	Duodenum Mucosa	Duodenum
38	chr17:20937800-20940600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr17:20938000-20940000	Weak transcription	Fetal Intestine Small	intestine
40	chr17:20938000-20940200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr17:20938000-20940200	Enhancers	Fetal Thymus	thymus
42	chr17:20938000-20940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr17:20938000-20941600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:20938000-20941800	Enhancers	Colon Smooth Muscle	Colon
45	chr17:20938200-20939800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr17:20938200-20940000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr17:20938200-20940200	Enhancers	Brain Anterior Caudate	brain
48	chr17:20938200-20940200	Weak transcription	Pancreas	Pancrea
49	chr17:20938200-20940200	Enhancers	HMEC	breast
50	chr17:20938200-20940400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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