Variant report

Variant	rs6514364
Chromosome Location	chr20:1369430-1369431
allele	A/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	chr20:1368016..1369679-chr20:1370045..1371864,2	K562	blood:
4	chr20:1296607..1299079-chr20:1367748..1369670,2	K562	blood:
5	chr20:1305143..1307185-chr20:1367459..1369677,2	MCF-7	breast:
6	chr20:1368185..1371576-chr20:1372390..1376018,4	MCF-7	breast:
7	chr20:1368376..1369903-chr20:1373657..1375943,2	K562	blood:

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

Extended variants
information (count: 100 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:99)

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];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]
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	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	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[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	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]
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[CHB][hapmap];1.00[CHD][hapmap];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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6514364	SIRPB2	cis	parietal	SCAN
rs6514364	PSMF1	cis	cerebellum	SCAN
rs6514364	PANK2	cis	cerebellum	SCAN
rs6514364	DDRGK1	cis	parietal	SCAN
rs6514364	FKBP1A	cis	parietal	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	chr20:1355600-1369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:1356400-1369600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr20:1356600-1369800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:1356800-1371800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr20:1358200-1369600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr20:1358400-1369800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr20:1358600-1369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr20:1358800-1370000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:1359200-1369600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr20:1359600-1369800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr20:1360000-1369800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr20:1360000-1369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr20:1363400-1370400	Weak transcription	Fetal Kidney	kidney
18	chr20:1363600-1369800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr20:1363600-1369800	Weak transcription	NH-A	brain
20	chr20:1363800-1369600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:1363800-1369800	Weak transcription	K562	blood
22	chr20:1363800-1371600	Weak transcription	Ovary	ovary
23	chr20:1364000-1369800	Weak transcription	Fetal Heart	heart
24	chr20:1364200-1369600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr20:1364600-1369600	Weak transcription	Fetal Intestine Large	intestine
26	chr20:1365000-1369600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr20:1365800-1369800	Weak transcription	Colonic Mucosa	Colon
28	chr20:1366200-1369600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr20:1367000-1370400	Weak transcription	Small Intestine	intestine
30	chr20:1367200-1369600	Weak transcription	Osteobl	bone
31	chr20:1367400-1369800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr20:1367400-1369800	Weak transcription	Aorta	Aorta
33	chr20:1367600-1369800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr20:1367600-1370000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr20:1368000-1369600	Enhancers	Psoas Muscle	Psoas
36	chr20:1368000-1372000	Genic enhancers	Primary monocytes fromperipheralblood	blood
37	chr20:1368200-1369800	Enhancers	Stomach Mucosa	stomach
38	chr20:1368400-1369600	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr20:1368400-1369800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:1368600-1369600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr20:1368600-1369600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr20:1368600-1369800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr20:1368600-1369800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr20:1368600-1370000	Genic enhancers	Muscle Satellite Cultured Cells	--
45	chr20:1368600-1370000	Enhancers	NHLF	lung
46	chr20:1368600-1370400	Genic enhancers	HepG2	liver
47	chr20:1368600-1370600	Flanking Active TSS	HUVEC	blood vessel
48	chr20:1368600-1370600	Enhancers	NHDF-Ad	bronchial
49	chr20:1368600-1370800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr20:1368800-1369600	Enhancers	Skeletal Muscle Female	skeletal muscle

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