Variant report

Variant	rs17193048
Chromosome Location	chr8:58055392-58055393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM110B-8	chr8:58055271-58055444	NONHSAT126727

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs16920056	0.81[EUR][1000 genomes]
rs16921688	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16921807	0.81[EUR][1000 genomes]
rs16921808	0.81[EUR][1000 genomes]
rs16921810	0.81[EUR][1000 genomes]
rs16921812	0.83[EUR][1000 genomes]
rs16921814	0.81[EUR][1000 genomes]
rs16921819	0.81[EUR][1000 genomes]
rs16921823	0.81[EUR][1000 genomes]
rs16921829	0.81[EUR][1000 genomes]
rs16921831	0.81[EUR][1000 genomes]
rs16921843	0.81[EUR][1000 genomes]
rs16921880	0.83[EUR][1000 genomes]
rs16922734	0.80[EUR][1000 genomes]
rs17194529	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17194792	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17194995	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17794451	0.83[ASN][1000 genomes]
rs17801390	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17802743	0.82[EUR][1000 genomes]
rs2005392	0.81[EUR][1000 genomes]
rs2088217	0.81[EUR][1000 genomes]
rs2101864	0.81[EUR][1000 genomes]
rs2318143	0.81[EUR][1000 genomes]
rs2318144	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2318145	0.81[EUR][1000 genomes]
rs2318146	0.81[EUR][1000 genomes]
rs2318147	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2318148	0.81[EUR][1000 genomes]
rs2873638	0.81[EUR][1000 genomes]
rs34804288	0.81[EUR][1000 genomes]
rs35840293	0.81[EUR][1000 genomes]
rs56066782	0.81[EUR][1000 genomes]
rs56201056	0.81[EUR][1000 genomes]
rs56211106	0.81[EUR][1000 genomes]
rs56235637	0.81[EUR][1000 genomes]
rs56825757	0.81[EUR][1000 genomes]
rs66667899	0.81[EUR][1000 genomes]
rs67002486	0.81[EUR][1000 genomes]
rs67996345	0.81[EUR][1000 genomes]
rs68079439	0.81[EUR][1000 genomes]
rs6981055	0.80[EUR][1000 genomes]
rs6982990	0.81[EUR][1000 genomes]
rs6987243	0.81[EUR][1000 genomes]
rs6991216	0.81[EUR][1000 genomes]
rs6995355	0.81[EUR][1000 genomes]
rs6995378	0.80[EUR][1000 genomes]
rs6995814	0.80[EUR][1000 genomes]
rs6998040	0.81[EUR][1000 genomes]
rs6999984	0.81[EUR][1000 genomes]
rs7000349	0.81[EUR][1000 genomes]
rs7004566	0.81[EUR][1000 genomes]
rs72649115	0.83[ASN][1000 genomes]
rs72649132	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72649133	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72649187	0.81[EUR][1000 genomes]
rs72649188	0.81[EUR][1000 genomes]
rs72649192	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72650811	0.81[EUR][1000 genomes]
rs73603874	0.81[EUR][1000 genomes]
rs73603877	0.81[EUR][1000 genomes]
rs73605816	0.81[EUR][1000 genomes]
rs7459925	0.81[EUR][1000 genomes]
rs7460059	0.81[EUR][1000 genomes]
rs7463453	0.81[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	nsv1029443	chr8:57748114-58057656	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1027125	chr8:57891279-58095884	Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2758161	chr8:57930392-58474449	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759618	chr8:57930392-58474449	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv533217	chr8:57991065-58789001	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv890933	chr8:58005923-58084006	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv890934	chr8:58037522-58112053	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv890935	chr8:58038406-58114743	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv12840	chr8:58046936-58196713	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv3693378	chr8:58051501-58128557	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv3432915	chr8:58055026-58271178	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17193048	RP11-513O17.2	cis	Nerve Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:58054800-58055400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
2	chr8:58054800-58055600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:58054800-58055600	Active TSS	Brain Anterior Caudate	brain
4	chr8:58054800-58055600	Bivalent Enhancer	Placenta	Placenta
5	chr8:58054800-58055800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
6	chr8:58054800-58055800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
7	chr8:58054800-58056000	Enhancers	Lung	lung
8	chr8:58054800-58056200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr8:58054800-58056400	Active TSS	Brain Germinal Matrix	brain
10	chr8:58054800-58057000	Active TSS	Fetal Brain Female	brain
11	chr8:58055000-58055400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr8:58055000-58055400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:58055000-58055400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:58055000-58055400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
15	chr8:58055000-58055400	Flanking Active TSS	Pancreas	Pancrea
16	chr8:58055000-58055400	Enhancers	Spleen	Spleen
17	chr8:58055000-58055400	Bivalent Enhancer	HMEC	breast
18	chr8:58055000-58055600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr8:58055000-58055600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr8:58055000-58055600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
21	chr8:58055000-58055600	Bivalent Enhancer	Left Ventricle	heart
22	chr8:58055000-58055600	Active TSS	Right Atrium	heart
23	chr8:58055000-58055600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
24	chr8:58055000-58055600	Bivalent Enhancer	Thymus	Thymus
25	chr8:58055000-58055800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr8:58055000-58056000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:58055000-58056000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr8:58055000-58056000	Bivalent Enhancer	Ovary	ovary
29	chr8:58055200-58055400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr8:58055200-58055400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
31	chr8:58055200-58055400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr8:58055200-58055400	Active TSS	Brain Angular Gyrus	brain
33	chr8:58055200-58055400	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
34	chr8:58055200-58055400	Bivalent/Poised TSS	Right Ventricle	heart
35	chr8:58055200-58055600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr8:58055200-58055600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:58055200-58055600	Active TSS	Brain Substantia Nigra	brain
38	chr8:58055200-58055600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr8:58055200-58055800	Bivalent Enhancer	Adipose Nuclei	Adipose
40	chr8:58055200-58055800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr8:58055200-58056200	Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links