Variant report

Variant	rs4902604
Chromosome Location	chr14:69054485-69054486
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69021201..69023551-chr14:69053894..69056000,2	MCF-7	breast:
2	chr14:68722408..68724336-chr14:69054457..69055958,2	K562	blood:
3	chr14:69053718..69056599-chr14:69063479..69065769,2	K562	blood:
4	chr14:68406708..68410646-chr14:69052499..69056687,4	MCF-7	breast:
5	chr14:69047861..69051902-chr14:69052585..69055305,4	MCF-7	breast:
6	chr14:69054452..69058686-chr14:69249853..69254831,4	MCF-7	breast:
7	chr14:69053766..69056397-chr14:69258298..69260703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12878761	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12894230	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1547012	0.91[CEU][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17829341	1.00[AFR][1000 genomes]
rs2257111	0.81[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2257116	0.81[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4531674	0.91[CEU][hapmap]
rs4899246	0.81[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59934413	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61985819	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61985820	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61985824	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61985825	0.85[EUR][1000 genomes];0.82[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	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1795754	chr14:69017623-69079110	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1832715	chr14:69017623-69079110	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4902604	PLEKHG3	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69047400-69060200	Weak transcription	Spleen	Spleen
2	chr14:69049800-69064000	Enhancers	Fetal Muscle Leg	muscle
3	chr14:69050200-69055000	Enhancers	Esophagus	oesophagus
4	chr14:69050200-69058800	Enhancers	Fetal Muscle Trunk	muscle
5	chr14:69050200-69058800	Enhancers	Placenta	Placenta
6	chr14:69051000-69055800	Enhancers	Fetal Thymus	thymus
7	chr14:69051000-69057000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:69051000-69057000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:69051200-69058200	Enhancers	NHDF-Ad	bronchial
10	chr14:69051200-69061800	Enhancers	Fetal Stomach	stomach
11	chr14:69051400-69057200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr14:69051400-69057400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr14:69051400-69058000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr14:69051600-69054800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:69051600-69057200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr14:69051800-69057600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr14:69052000-69057600	Enhancers	Fetal Lung	lung
18	chr14:69052000-69057800	Enhancers	Colon Smooth Muscle	Colon
19	chr14:69052200-69054600	Enhancers	Stomach Mucosa	stomach
20	chr14:69052200-69058000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr14:69052400-69054800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr14:69052600-69054800	Enhancers	Colonic Mucosa	Colon
23	chr14:69052600-69055600	Weak transcription	HepG2	liver
24	chr14:69052600-69057400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr14:69052600-69057800	Enhancers	Adipose Nuclei	Adipose
26	chr14:69052600-69060400	Weak transcription	Osteobl	bone
27	chr14:69052800-69055200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr14:69052800-69057000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr14:69052800-69059600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr14:69052800-69064800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr14:69053000-69054800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:69053000-69054800	Enhancers	Fetal Intestine Large	intestine
33	chr14:69053000-69055000	Enhancers	Fetal Brain Female	brain
34	chr14:69053000-69055000	Enhancers	Hela-S3	cervix
35	chr14:69053000-69056800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:69053200-69054600	Enhancers	NHEK	skin
37	chr14:69053200-69054800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:69053200-69054800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr14:69053200-69054800	Enhancers	Lung	lung
40	chr14:69053200-69056600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:69053400-69055600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr14:69053400-69056800	Weak transcription	Pancreas	Pancrea
43	chr14:69053400-69064800	Weak transcription	Brain Substantia Nigra	brain
44	chr14:69053600-69054600	Enhancers	HMEC	breast
45	chr14:69053600-69054600	Enhancers	NHLF	lung
46	chr14:69053600-69054800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:69053600-69055000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr14:69053600-69055000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr14:69053600-69055200	Enhancers	HSMM	muscle
50	chr14:69053600-69056200	Enhancers	HUES48 Cell Line	embryonic stem cell

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