Variant report

Variant	rs916962
Chromosome Location	chr14:68993578-68993579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:7052631..7053153-chr14:68993272..68993773,2	Hela-S3	cervix:
2	chr14:68990794..68994075-chr14:69256455..69260885,5	MCF-7	breast:
3	chr14:68982120..68984316-chr14:68992913..68995083,2	MCF-7	breast:
4	chr14:68987292..68989067-chr14:68991224..68994887,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111678	Chromatin interaction
ENSG00000185650	Chromatin interaction
ENSG00000238923	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10134446	0.88[JPT][hapmap]
rs1023529	0.86[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs11158749	0.94[JPT][hapmap]
rs1476586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040782	0.85[AMR][1000 genomes]
rs2078316	0.82[JPT][hapmap]
rs2079211	0.92[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs2107341	0.88[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes]
rs2158358	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2189517	0.94[JPT][hapmap]
rs2244814	0.90[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap]
rs2247048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525522	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525523	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525524	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842325	0.92[CHB][hapmap];0.85[AMR][1000 genomes]
rs2842329	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2842331	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842338	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140266	0.88[JPT][hapmap]
rs757370	0.91[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs929285	0.92[CHB][hapmap];0.84[AMR][1000 genomes]
rs9323513	0.93[JPT][hapmap]
rs9323514	0.94[JPT][hapmap]

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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	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
3	nsv1048064	chr14:68991041-69012766	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs916962	PLEKHG3	cis	cerebellum	SCAN
rs916962	ATP6V1D	cis	cerebellum	SCAN
rs916962	FAM71D	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68985800-68994800	Weak transcription	Aorta	Aorta
2	chr14:68987400-68993600	Enhancers	HSMM	muscle
3	chr14:68987400-68996200	Enhancers	Pancreas	Pancrea
4	chr14:68988200-68993600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr14:68988600-68993800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:68989800-68993800	Weak transcription	Primary B cells from cord blood	blood
7	chr14:68990000-68994200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:68990000-68995400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr14:68990000-68995600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:68990000-68996000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr14:68990200-68993800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr14:68990200-68993800	Enhancers	HSMMtube	muscle
13	chr14:68990400-68993600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr14:68991200-68994000	Weak transcription	Fetal Lung	lung
15	chr14:68991600-68994400	Enhancers	Lung	lung
16	chr14:68991800-68994000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:68991800-68994200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:68991800-68994200	Weak transcription	Thymus	Thymus
19	chr14:68992000-68994000	Weak transcription	NHLF	lung
20	chr14:68992400-68994600	Weak transcription	Primary T cells from cord blood	blood
21	chr14:68992600-68996000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr14:68992800-68993600	Enhancers	HUVEC	blood vessel
23	chr14:68993000-68993600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr14:68993000-68993800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr14:68993000-68993800	Enhancers	Stomach Mucosa	stomach
26	chr14:68993000-68993800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr14:68993000-68994000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr14:68993000-68994000	Flanking Active TSS	Hela-S3	cervix
29	chr14:68993000-68994200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr14:68993000-68994200	Enhancers	NHEK	skin
31	chr14:68993000-68994400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr14:68993000-68994400	Enhancers	HMEC	breast
33	chr14:68993000-68994400	Enhancers	NHDF-Ad	bronchial
34	chr14:68993000-68994600	Enhancers	A549	lung
35	chr14:68993000-68994600	Enhancers	NH-A	brain
36	chr14:68993000-68995000	Enhancers	Fetal Intestine Large	intestine
37	chr14:68993000-68995000	Enhancers	Fetal Kidney	kidney
38	chr14:68993000-68995800	Enhancers	Liver	Liver
39	chr14:68993200-68993600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr14:68993200-68993600	Enhancers	Gastric	stomach
41	chr14:68993200-68993600	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr14:68993200-68993800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr14:68993200-68993800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr14:68993200-68993800	Genic enhancers	Fetal Intestine Small	intestine
45	chr14:68993200-68993800	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr14:68993200-68994200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr14:68993200-68994200	Enhancers	Brain Anterior Caudate	brain
48	chr14:68993200-68994200	Enhancers	Esophagus	oesophagus
49	chr14:68993200-68994400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr14:68993200-68994400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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