Variant report

Variant	rs1998120
Chromosome Location	chr14:65175364-65175365
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65174479..65176413-chr14:65184169..65186446,2	K562	blood:
2	chr14:65168373..65176902-chr14:65220182..65231670,21	MCF-7	breast:
3	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:
4	chr14:65170433..65175465-chr14:65207632..65214317,8	MCF-7	breast:
5	chr14:65168335..65178043-chr14:65220677..65234710,31	MCF-7	breast:
6	chr14:65173952..65176818-chr14:65213044..65215895,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126822	Chromatin interaction
ENSG00000070182	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs17179970	0.87[ASN][1000 genomes]
rs17179984	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17180090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17767188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17767206	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1985465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1985466	0.96[ASN][1000 genomes]
rs229603	0.94[EUR][1000 genomes]
rs229624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs229625	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229644	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs229650	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229651	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229659	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs229660	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs229662	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229663	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229664	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs229665	0.86[EUR][1000 genomes]
rs41301473	0.91[ASN][1000 genomes]
rs41307086	0.87[ASN][1000 genomes]
rs58789159	0.91[ASN][1000 genomes]
rs73273513	0.96[ASN][1000 genomes]
rs73273517	1.00[ASN][1000 genomes]
rs73273524	0.91[ASN][1000 genomes]
rs73273534	0.91[ASN][1000 genomes]
rs73273536	0.91[ASN][1000 genomes]
rs73273546	0.83[ASN][1000 genomes]
rs73273549	0.91[ASN][1000 genomes]
rs754435	0.91[ASN][1000 genomes]
rs872296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][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	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1998120	PLEKHG3	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65170000-65176600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr14:65171800-65177200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr14:65172400-65176800	Enhancers	Small Intestine	intestine
4	chr14:65172800-65175600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:65172800-65176400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:65172800-65176400	Enhancers	Stomach Mucosa	stomach
7	chr14:65172800-65178000	Enhancers	Fetal Heart	heart
8	chr14:65173000-65176400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr14:65173000-65177000	Enhancers	Pancreas	Pancrea
10	chr14:65173000-65177000	Enhancers	Right Atrium	heart
11	chr14:65173000-65177600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr14:65173200-65175600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr14:65173200-65175800	Enhancers	Brain Germinal Matrix	brain
14	chr14:65173200-65176400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr14:65173200-65177000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr14:65173200-65178000	Enhancers	Spleen	Spleen
17	chr14:65173400-65175600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr14:65173400-65178000	Enhancers	Adipose Nuclei	Adipose
19	chr14:65173600-65175400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:65173600-65175800	Weak transcription	Psoas Muscle	Psoas
21	chr14:65173600-65175800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr14:65173600-65176000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:65173600-65176200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr14:65173600-65176400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr14:65173600-65176400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr14:65173800-65176400	Genic enhancers	Fetal Stomach	stomach
27	chr14:65173800-65176800	Enhancers	Esophagus	oesophagus
28	chr14:65173800-65178000	Enhancers	Ovary	ovary
29	chr14:65173800-65179000	Enhancers	Liver	Liver
30	chr14:65174000-65175800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:65174000-65176000	Enhancers	Fetal Lung	lung
32	chr14:65174000-65176400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:65174200-65175600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr14:65174200-65176400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr14:65174400-65175400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr14:65174400-65175400	Enhancers	HSMM	muscle
37	chr14:65174400-65176200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:65174400-65176800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:65174400-65178000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr14:65174600-65175400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr14:65174600-65175400	Flanking Active TSS	NH-A	brain
42	chr14:65174600-65175400	Flanking Active TSS	Osteobl	bone
43	chr14:65174600-65175600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr14:65174600-65175600	Weak transcription	Right Ventricle	heart
45	chr14:65174600-65175800	Flanking Active TSS	HMEC	breast
46	chr14:65174600-65176200	Enhancers	Colonic Mucosa	Colon
47	chr14:65174600-65176800	Enhancers	Gastric	stomach
48	chr14:65174600-65177000	Weak transcription	Aorta	Aorta
49	chr14:65174800-65175400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr14:65174800-65175600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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