Variant report

Variant	rs8020262
Chromosome Location	chr14:67886117-67886118
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:67882986..67884493-chr14:67884717..67887136,2	K562	blood:
2	chr14:67885398..67886397-chr14:67893582..67894143,2	K562	blood:
3	chr14:67879811..67882553-chr14:67883761..67886791,3	K562	blood:
4	chr14:67884151..67886526-chr14:67911099..67913926,2	K562	blood:
5	chr14:67885208..67887110-chr14:68037117..68038888,2	MCF-7	breast:
6	chr14:67825763..67827474-chr14:67883960..67886590,2	K562	blood:

Variant related genes	Relation type
ENSG00000134001	Chromatin interaction
ENSG00000100554	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10131212	0.85[CHD][hapmap]
rs10132093	0.81[JPT][hapmap]
rs10137094	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10137557	0.81[JPT][hapmap]
rs10138755	0.80[JPT][hapmap]
rs10138824	0.85[CHD][hapmap]
rs10141879	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs10144090	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10144401	0.83[CHD][hapmap]
rs10144417	0.83[CHD][hapmap]
rs10145586	0.82[JPT][hapmap]
rs10146663	0.83[CHD][hapmap]
rs10146722	0.81[JPT][hapmap]
rs10147852	0.85[CHD][hapmap]
rs10148070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10150902	0.83[CHD][hapmap]
rs1045060	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs1078194	0.87[JPT][hapmap]
rs12323911	0.83[CHD][hapmap]
rs12590956	0.87[JPT][hapmap]
rs1535491	0.85[CHD][hapmap]
rs1555853	0.90[CHD][hapmap];0.87[JPT][hapmap]
rs17248526	0.85[CHD][hapmap]
rs17248895	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2031563	0.83[CHD][hapmap]
rs2146229	0.85[CHD][hapmap]
rs2146230	0.85[CHD][hapmap]
rs2296560	0.85[CHD][hapmap]
rs3759755	0.83[CHD][hapmap]
rs3818467	0.83[CHD][hapmap]
rs3818468	0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4143909	0.82[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6573763	0.89[JPT][hapmap]
rs7152903	0.85[CHD][hapmap]
rs7156441	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs8004148	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs8004267	0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8004332	0.88[CHD][hapmap];0.83[JPT][hapmap]
rs8004864	0.83[JPT][hapmap]
rs8006519	0.80[CHD][hapmap]
rs8007033	0.85[CHD][hapmap]
rs8007618	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs8008619	0.83[CHD][hapmap]
rs8008724	0.83[CHD][hapmap]
rs8015950	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8016037	0.85[CHD][hapmap]
rs8021730	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8021896	0.85[CHD][hapmap]
rs9323497	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751285	chr14:67364747-67886781	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1045518	chr14:67529049-67959582	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1054389	chr14:67804987-67922598	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv542121	chr14:67804987-67922598	Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv1319	chr14:67863561-67908725	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	diseases
9	esv3487440	chr14:67863754-67892047	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	esv3487442	chr14:67863758-67892045	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8020262	RAB15	cis	parietal	SCAN
rs8020262	ATP6V1D	cis	Skin Sun Exposed Lower leg	GTEx
rs8020262	FAM71D	cis	cerebellum	SCAN
rs8020262	EIF2S1	cis	lymphoblastoid	seeQTL
rs8020262	SRSF5	cis	cerebellum	SCAN
rs8020262	ASCL1	trans	lymphoblastoid	seeQTL
rs8020262	EIF2S1	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67879200-67886600	Weak transcription	Spleen	Spleen
2	chr14:67879600-67888400	Weak transcription	Fetal Heart	heart
3	chr14:67881400-67892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:67882400-67887400	Enhancers	Placenta	Placenta
5	chr14:67884800-67887000	Enhancers	HMEC	breast
6	chr14:67885000-67886200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr14:67885000-67886200	Enhancers	A549	lung
8	chr14:67885000-67886200	Flanking Active TSS	Hela-S3	cervix
9	chr14:67885000-67887000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:67885000-67887200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:67885000-67887400	Enhancers	Stomach Mucosa	stomach
12	chr14:67885200-67886200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:67885200-67886200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr14:67885200-67886200	Enhancers	HUVEC	blood vessel
15	chr14:67885200-67886400	Enhancers	Fetal Intestine Large	intestine
16	chr14:67885200-67887000	Enhancers	Fetal Intestine Small	intestine
17	chr14:67885400-67886200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:67885400-67886200	Enhancers	Placenta Amnion	Placenta Amnion
19	chr14:67885400-67886200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr14:67885400-67886200	Enhancers	NH-A	brain
21	chr14:67885400-67886200	Flanking Active TSS	NHEK	skin
22	chr14:67885400-67887000	Enhancers	Duodenum Mucosa	Duodenum
23	chr14:67885400-67887000	Enhancers	Esophagus	oesophagus
24	chr14:67885400-67887000	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr14:67885800-67886800	Weak transcription	Gastric	stomach
26	chr14:67885800-67886800	Weak transcription	Pancreas	Pancrea
27	chr14:67886000-67886200	Flanking Active TSS	K562	blood
28	chr14:67886000-67889800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr14:67886000-67894800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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