Variant report

Variant	rs4624992
Chromosome Location	chr8:11291597-11291598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8orf12-1	chr8:11291429-11291644	NONHSAT125054
2	lnc-C8orf12-1	chr8:11291429-11291644	NR_026814
3	lnc-C8orf12-1	chr8:11291429-11291644	NONHSAT125056

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17153245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17153280	1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28478078	0.88[EUR][1000 genomes]
rs56004143	0.88[EUR][1000 genomes]
rs57738273	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60493532	0.82[EUR][1000 genomes]
rs60838274	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61707317	0.82[EUR][1000 genomes]
rs6998356	0.94[EUR][1000 genomes]
rs7014311	1.00[GIH][hapmap];0.88[EUR][1000 genomes]
rs73663144	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73663146	0.88[EUR][1000 genomes]

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	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
7	nsv470183	chr8:11236975-11307118	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv465465	chr8:11245064-11307118	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv610275	chr8:11245064-11307118	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv522860	chr8:11253879-11330364	Bivalent/Poised TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv890357	chr8:11286146-11330364	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4624992	ESF1	trans	brain	seeQTL
rs4624992	ARAP2	trans	brain	seeQTL
rs4624992	KRCC1	trans	brain	seeQTL
rs4624992	GOLIM4	trans	brain	seeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11280600-11308800	Weak transcription	Primary B cells from cord blood	blood
2	chr8:11280800-11297600	Weak transcription	Spleen	Spleen
3	chr8:11286000-11295200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:11286200-11306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:11286600-11296200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:11287400-11296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:11287400-11296400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:11287400-11297600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:11287600-11291600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr8:11287800-11313600	Weak transcription	Right Atrium	heart
13	chr8:11288000-11297600	Weak transcription	HSMM	muscle
14	chr8:11288200-11300200	Weak transcription	Brain Hippocampus Middle	brain
15	chr8:11289000-11295400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:11289000-11295600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:11289600-11291600	Weak transcription	Thymus	Thymus
18	chr8:11289800-11299600	Weak transcription	Brain Anterior Caudate	brain
19	chr8:11289800-11305800	Weak transcription	Osteobl	bone
20	chr8:11290800-11293000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr8:11290800-11293800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:11290800-11294000	Enhancers	Fetal Heart	heart
23	chr8:11291000-11291600	Enhancers	Brain Angular Gyrus	brain
24	chr8:11291000-11291800	Strong transcription	NHEK	skin
25	chr8:11291000-11292200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:11291000-11292400	Enhancers	Pancreas	Pancrea
27	chr8:11291000-11292600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:11291000-11295000	Enhancers	Fetal Thymus	thymus
29	chr8:11291200-11291600	Enhancers	Brain Cingulate Gyrus	brain
30	chr8:11291200-11292000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr8:11291200-11292200	Enhancers	Stomach Mucosa	stomach
32	chr8:11291200-11292800	Enhancers	Gastric	stomach
33	chr8:11291200-11296200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:11291400-11292000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr8:11291400-11292200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr8:11291400-11292200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:11291400-11292200	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links