Variant report

Variant	rs4813115
Chromosome Location	chr20:1364154-1364155
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1362022..1364413-chr20:1372560..1374145,2	MCF-7	breast:
2	chr20:1355645..1357681-chr20:1363230..1365988,2	K562	blood:
3	chr20:1360923..1364205-chr20:1370000..1374506,6	K562	blood:
4	chr20:1305375..1307860-chr20:1363586..1366109,2	K562	blood:

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

Extended variants
information (count: 103 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10485824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11087048	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11697322	1.00[CHB][hapmap]
rs11697395	1.00[CHB][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]
rs16995332	1.00[CHB][hapmap]
rs17793560	1.00[CHB][hapmap]
rs17794135	1.00[CHB][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]
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]
rs4536713	1.00[ASN][1000 genomes]
rs45512895	1.00[ASN][1000 genomes]
rs4577347	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[ASN][1000 genomes]
rs6033660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6033672	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6033871	1.00[CHB][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[ASN][1000 genomes]
rs6042000	1.00[ASN][1000 genomes]
rs6042506	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042550	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042568	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6042574	1.00[CHB][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]
rs6078575	1.00[CHB][hapmap]
rs6105031	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	1.00[CHB][hapmap]
rs6109437	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109511	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6109605	1.00[YRI][hapmap]
rs6109623	0.86[ASW][hapmap];0.92[LWK][hapmap];0.95[YRI][hapmap]
rs6109740	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]
rs6109784	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	1.00[CHB][hapmap]
rs6109989	1.00[CHB][hapmap]
rs6110189	1.00[CHB][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[ASN][1000 genomes]
rs715217	1.00[CHB][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]
rs733233	0.80[ASW][hapmap]
rs73579382	1.00[ASN][1000 genomes]
rs73581208	1.00[ASN][1000 genomes]
rs747611	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117563	1.00[CHB][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
rs4813115	PSMF1	cis	cerebellum	SCAN
rs4813115	PANK2	cis	cerebellum	SCAN
rs4813115	FKBP1A	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 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	chr20:1348000-1366800	Strong transcription	Dnd41	blood
5	chr20:1353200-1369400	Weak transcription	Brain Germinal Matrix	brain
6	chr20:1354400-1371200	Weak transcription	Fetal Brain Male	brain
7	chr20:1355400-1369000	Weak transcription	Fetal Brain Female	brain
8	chr20:1355600-1366400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr20:1355600-1369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:1356400-1365600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr20:1356400-1369600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr20:1356600-1369800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr20:1356800-1365400	Weak transcription	Colonic Mucosa	Colon
14	chr20:1356800-1369200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr20:1356800-1371800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr20:1357600-1369000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr20:1357800-1365800	Genic enhancers	HepG2	liver
18	chr20:1358000-1367000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr20:1358200-1369600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr20:1358400-1369800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr20:1358600-1366800	Weak transcription	Aorta	Aorta
22	chr20:1358600-1369800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr20:1358800-1370000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr20:1359000-1366400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr20:1359000-1369000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr20:1359200-1364200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:1359200-1369600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr20:1359600-1369800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr20:1360000-1369800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr20:1360000-1369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr20:1360200-1366400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr20:1360600-1367200	Enhancers	Stomach Mucosa	stomach
33	chr20:1361200-1369000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr20:1361800-1367600	Enhancers	Adipose Nuclei	Adipose
35	chr20:1362000-1367400	Genic enhancers	Primary T cells from cord blood	blood
36	chr20:1362200-1364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr20:1362200-1364200	Enhancers	Rectal Smooth Muscle	rectum
38	chr20:1362400-1369000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr20:1362600-1364400	Genic enhancers	Brain Anterior Caudate	brain
40	chr20:1362600-1364400	Enhancers	Osteobl	bone
41	chr20:1362600-1364600	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr20:1362600-1364800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr20:1362600-1367400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr20:1362600-1367600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr20:1362800-1364200	Enhancers	Lung	lung
46	chr20:1362800-1364200	Enhancers	Right Atrium	heart
47	chr20:1362800-1364600	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr20:1362800-1364600	Enhancers	Left Ventricle	heart
49	chr20:1362800-1364800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr20:1362800-1364800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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