Variant report

Variant	rs8117563
Chromosome Location	chr20:1346162-1346163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:1342733..1346538-chr20:1346730..1348798,3	K562	blood:
2	chr20:1346000..1350154-chr20:1350167..1354202,4	K562	blood:
3	chr20:1343934..1346558-chr20:1353759..1356029,2	MCF-7	breast:
4	chr20:1343841..1348695-chr20:1349294..1353469,5	K562	blood:
5	chr20:1345564..1348128-chr20:1371036..1372870,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FKBP1A-2	chr20:1346028-1346201	l_2057_chr20:1333800-1352641_testes

No data

Variant related genes	Relation type
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11087048	1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11697973	1.00[ASN][1000 genomes]
rs11699494	1.00[CHB][hapmap]
rs13163	1.00[CHB][hapmap]
rs13433171	1.00[ASN][1000 genomes]
rs16994239	1.00[CHB][hapmap]
rs16994549	1.00[CHB][hapmap]
rs16995146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1883933	1.00[CHB][hapmap]
rs1884390	1.00[CHB][hapmap]
rs2064645	1.00[CHB][hapmap]
rs2064646	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2249832	1.00[CHB][hapmap]
rs2250091	1.00[CHB][hapmap]
rs2253429	1.00[CHB][hapmap]
rs2253431	1.00[CHB][hapmap]
rs2253693	1.00[CHB][hapmap]
rs2253698	1.00[CHB][hapmap]
rs2256095	1.00[CHB][hapmap]
rs2256229	1.00[CHB][hapmap]
rs2256240	1.00[CHB][hapmap]
rs2256243	1.00[CHB][hapmap]
rs2256250	1.00[CHB][hapmap]
rs2256251	1.00[CHB][hapmap]
rs2263656	1.00[CHB][hapmap]
rs2873522	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4536713	1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4813115	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4814102	1.00[CHB][hapmap]
rs56035174	1.00[ASN][1000 genomes]
rs57806058	1.00[ASN][1000 genomes]
rs59377624	1.00[ASN][1000 genomes]
rs59681252	1.00[ASN][1000 genomes]
rs6033534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033554	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6033660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033672	1.00[ASN][1000 genomes]
rs6033871	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6033896	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033914	1.00[CHB][hapmap]
rs6033935	1.00[CHB][hapmap]
rs6041382	1.00[ASN][1000 genomes]
rs6041689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6041716	1.00[CHB][hapmap];0.91[LWK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6041734	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs6041827	0.86[YRI][hapmap]
rs6042000	1.00[ASN][1000 genomes]
rs6042506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042550	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042574	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6042578	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042585	1.00[CHB][hapmap]
rs6042588	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6105101	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109740	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6109784	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6110189	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6110193	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs62187542	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62187543	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6514339	1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes]
rs6514364	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs715217	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7271240	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs73067251	1.00[ASN][1000 genomes]
rs73069188	1.00[ASN][1000 genomes]
rs73076965	1.00[ASN][1000 genomes]
rs73076966	1.00[ASN][1000 genomes]
rs73579382	1.00[ASN][1000 genomes]
rs73581208	1.00[ASN][1000 genomes]
rs747611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8117744	1.00[ASN][1000 genomes]
rs8118276	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8119259	1.00[ASN][1000 genomes]
rs912113	1.00[CHB][hapmap]
rs958839	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8117563	RBCK1	cis	cerebellum	SCAN
rs8117563	PANK2	cis	cerebellum	SCAN
rs8117563	RAD21L1	cis	cerebellum	SCAN
rs8117563	DDRGK1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1310000-1348800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:1323000-1350600	Weak transcription	Fetal Brain Male	brain
3	chr20:1323400-1354000	Weak transcription	Fetal Heart	heart
4	chr20:1326000-1350600	Weak transcription	Right Atrium	heart
5	chr20:1326800-1348200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr20:1327600-1372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:1331600-1349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:1331600-1358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr20:1332400-1348400	Weak transcription	Psoas Muscle	Psoas
10	chr20:1332400-1349200	Weak transcription	Colonic Mucosa	Colon
11	chr20:1333200-1349000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:1336200-1348000	Weak transcription	Aorta	Aorta
13	chr20:1336200-1348000	Weak transcription	Brain Germinal Matrix	brain
14	chr20:1336200-1348000	Weak transcription	Esophagus	oesophagus
15	chr20:1336200-1350600	Weak transcription	Right Ventricle	heart
16	chr20:1336200-1361800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr20:1336400-1350600	Weak transcription	Fetal Lung	lung
18	chr20:1336400-1355600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr20:1337600-1349400	Strong transcription	Fetal Muscle Leg	muscle
21	chr20:1337800-1348000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr20:1338400-1348000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:1338600-1346400	Strong transcription	NHEK	skin
24	chr20:1338600-1354800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr20:1339000-1348800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:1339200-1348000	Weak transcription	Fetal Kidney	kidney
27	chr20:1339200-1348200	Weak transcription	Brain Angular Gyrus	brain
28	chr20:1339200-1348200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr20:1339200-1350600	Weak transcription	Pancreas	Pancrea
30	chr20:1340000-1349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr20:1340200-1349000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:1340200-1349000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:1340600-1346600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr20:1341200-1346200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr20:1341200-1347800	Weak transcription	Osteobl	bone
36	chr20:1341200-1348000	Weak transcription	Brain Hippocampus Middle	brain
37	chr20:1341200-1348000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr20:1341200-1350400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr20:1341200-1351000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr20:1341200-1351600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr20:1341400-1348000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr20:1341400-1348000	Weak transcription	Ovary	ovary
43	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
44	chr20:1341600-1348000	Weak transcription	Fetal Brain Female	brain
45	chr20:1341600-1350600	Weak transcription	Brain Substantia Nigra	brain
46	chr20:1341600-1350800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr20:1341800-1346400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr20:1341800-1347800	Weak transcription	Placenta	Placenta
49	chr20:1341800-1350800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr20:1342200-1346800	Strong transcription	Fetal Stomach	stomach

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