Variant report

Variant	rs8009162
Chromosome Location	chr14:25447887-25447888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GZMB-1	chr14:25447874-25448099	uc_358_-
2	lnc-RP11-80A15.1.1-7	chr14:25447874-25448099	uc_358_+

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10131274	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs10132944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10134048	0.81[ASN][1000 genomes]
rs10134818	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10137405	0.90[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10145076	0.81[ASN][1000 genomes]
rs11159009	0.99[ASN][1000 genomes]
rs11625143	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1555598	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17109366	0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17109401	0.81[ASN][1000 genomes]
rs17185460	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2038700	0.80[AMR][1000 genomes]
rs2093714	0.82[CHD][hapmap]
rs7141943	0.80[AMR][1000 genomes]
rs7143179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155878	0.80[ASN][1000 genomes]
rs7157481	1.00[ASW][hapmap];0.86[CEU][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7161210	0.81[ASN][1000 genomes]
rs724116	0.80[ASN][1000 genomes]
rs8011948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8017228	0.80[AMR][1000 genomes]
rs8017710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8021478	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9323580	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901508	chr14:25365505-25451903	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1041051	chr14:25388230-25480511	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1047792	chr14:25388933-25503799	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8009162	CIDEB	cis	lymphoblastoid	GTEx
rs8009162	STXBP6	cis	parietal	SCAN
rs8009162	PKMYT1	trans	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25424600-25460600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr14:25430000-25465800	Weak transcription	Lung	lung
3	chr14:25436200-25448000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:25436200-25451200	Weak transcription	A549	lung
5	chr14:25436600-25454200	Weak transcription	Fetal Muscle Leg	muscle
6	chr14:25436600-25454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:25436600-25455400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:25436800-25451200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr14:25437200-25448000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:25438200-25448000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:25441000-25454200	Weak transcription	Fetal Brain Male	brain
12	chr14:25443800-25451400	Weak transcription	Left Ventricle	heart
13	chr14:25443800-25451400	Weak transcription	HSMM	muscle
14	chr14:25444000-25450400	Weak transcription	Pancreas	Pancrea
15	chr14:25444000-25451800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr14:25444200-25448800	Weak transcription	Fetal Lung	lung
17	chr14:25444200-25454600	Weak transcription	Right Atrium	heart
18	chr14:25444800-25449000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:25444800-25450400	Enhancers	Fetal Intestine Large	intestine
20	chr14:25445000-25450600	Enhancers	Fetal Intestine Small	intestine
21	chr14:25445200-25454200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr14:25445400-25448200	Weak transcription	Fetal Heart	heart
23	chr14:25445400-25451600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr14:25445600-25454600	Weak transcription	Brain Anterior Caudate	brain
25	chr14:25446800-25448400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr14:25446800-25452800	Enhancers	HepG2	liver
27	chr14:25447000-25448200	Weak transcription	Psoas Muscle	Psoas
28	chr14:25447000-25449000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr14:25447400-25448000	Enhancers	Duodenum Mucosa	Duodenum
30	chr14:25447400-25448000	Enhancers	Small Intestine	intestine
31	chr14:25447400-25449000	Enhancers	GM12878-XiMat	blood
32	chr14:25447800-25449200	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links