Variant report

Variant	rs6109740
Chromosome Location	chr20:1369825-1369826
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1368035..1371402-chr20:1444854..1448732,3	MCF-7	breast:
2	chr20:1296232..1299079-chr20:1367748..1370124,3	K562	blood:
3	chr20:1304653..1308515-chr20:1369739..1375969,7	MCF-7	breast:
4	chr20:1368185..1371576-chr20:1372390..1376018,4	MCF-7	breast:
5	chr20:1368376..1369903-chr20:1373657..1375943,2	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000234684	Chromatin interaction
ENSG00000088832	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11087048	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11697973	1.00[ASN][1000 genomes]
rs11697987	1.00[ASN][1000 genomes]
rs11698000	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]
rs16995228	1.00[ASN][1000 genomes]
rs16995310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16995332	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
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]
rs33999287	1.00[ASN][1000 genomes]
rs35442028	1.00[ASN][1000 genomes]
rs4536713	1.00[ASN][1000 genomes]
rs45512895	1.00[ASN][1000 genomes]
rs4577347	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4813115	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];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	1.00[CHB][hapmap];1.00[CHD][hapmap];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]
rs6041717	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
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]
rs6042676	1.00[CHB][hapmap]
rs6042689	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6078575	1.00[CHB][hapmap]
rs6105031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];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]
rs6109605	0.94[YRI][hapmap]
rs6109623	0.93[ASW][hapmap];0.94[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs6109784	1.00[CHB][hapmap];0.82[AMR][1000 genomes];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	1.00[ASN][1000 genomes]
rs62187543	1.00[ASN][1000 genomes]
rs62623705	1.00[ASN][1000 genomes]
rs6514337	1.00[CHB][hapmap];1.00[ASN][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]
rs7274052	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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117563	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6109740	FKBP1A	cis	multi-tissue	Pritchard
rs6109740	PSMF1	cis	cerebellum	SCAN
rs6109740	PANK2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1327600-1372200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:1336400-1370400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:1341400-1370600	Weak transcription	Hela-S3	cervix
4	chr20:1354400-1371200	Weak transcription	Fetal Brain Male	brain
5	chr20:1356800-1371800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr20:1358800-1370000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:1363400-1370400	Weak transcription	Fetal Kidney	kidney
8	chr20:1363800-1371600	Weak transcription	Ovary	ovary
9	chr20:1367000-1370400	Weak transcription	Small Intestine	intestine
10	chr20:1367600-1370000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr20:1368000-1372000	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr20:1368600-1370000	Genic enhancers	Muscle Satellite Cultured Cells	--
13	chr20:1368600-1370000	Enhancers	NHLF	lung
14	chr20:1368600-1370400	Genic enhancers	HepG2	liver
15	chr20:1368600-1370600	Flanking Active TSS	HUVEC	blood vessel
16	chr20:1368600-1370600	Enhancers	NHDF-Ad	bronchial
17	chr20:1368600-1370800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr20:1368800-1370400	Enhancers	HSMMtube	muscle
19	chr20:1368800-1370800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr20:1368800-1371200	Enhancers	Left Ventricle	heart
21	chr20:1368800-1371400	Enhancers	Primary B cells from peripheral blood	blood
22	chr20:1368800-1372000	Enhancers	Brain Substantia Nigra	brain
23	chr20:1369000-1370000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr20:1369000-1370000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr20:1369000-1370000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr20:1369000-1370000	Enhancers	Fetal Brain Female	brain
27	chr20:1369000-1370000	Strong transcription	Fetal Intestine Small	intestine
28	chr20:1369000-1370200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
29	chr20:1369000-1370200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr20:1369000-1370200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr20:1369000-1370400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr20:1369000-1370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:1369000-1370400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr20:1369000-1370400	Enhancers	Gastric	stomach
35	chr20:1369000-1370600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr20:1369000-1370600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr20:1369000-1370600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
38	chr20:1369000-1370800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr20:1369000-1370800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr20:1369000-1370800	Transcr. at gene 5' and 3'	Dnd41	blood
41	chr20:1369000-1371200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr20:1369000-1371200	Enhancers	Brain Hippocampus Middle	brain
43	chr20:1369000-1371400	Enhancers	Colon Smooth Muscle	Colon
44	chr20:1369000-1371600	Enhancers	Pancreas	Pancrea
45	chr20:1369000-1371600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr20:1369000-1371800	Enhancers	H1 Cell Line	embryonic stem cell
47	chr20:1369000-1372000	Genic enhancers	Fetal Stomach	stomach
48	chr20:1369000-1372200	Genic enhancers	Fetal Lung	lung
49	chr20:1369000-1372400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr20:1369000-1373200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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