Variant report

Variant	rs58963621
Chromosome Location	chr16:70559151-70559152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:70558792-70559155	GM12891	blood:	n/a	n/a
2	POLR2A	chr16:70558920-70559318	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr16:70555921-70559826	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:70556975-70559531	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:70556908-70559399	K562	blood:	n/a	n/a
6	POLR2A	chr16:70558756-70559218	GM12892	blood:	n/a	n/a
7	TCF7L2	chr16:70558369-70559192	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr16:70556081-70559643	GM12892	blood:	n/a	n/a
9	POLR2A	chr16:70558792-70559303	PFSK-1	brain:	n/a	n/a
10	HEY1	chr16:70558920-70559346	HepG2	liver:	n/a	n/a
11	POLR2A	chr16:70556580-70559247	GM19193	blood:	n/a	n/a
12	POLR2A	chr16:70558789-70559576	MCF-7	breast:	n/a	n/a
13	MYC	chr16:70559071-70559294	MCF10A-Er-Src	breast:	n/a	n/a
14	YY1	chr16:70559118-70559255	K562	blood:	n/a	n/a
15	HEY1	chr16:70558780-70559724	K562	blood:	n/a	n/a
16	MYC	chr16:70559102-70559239	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr16:70558801-70559303	HL-60	blood:	n/a	n/a
18	POLR2A	chr16:70556548-70559364	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr16:70558966-70559520	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr16:70558785-70559189	Hela-S3	cervix:	n/a	n/a
21	MAX	chr16:70558900-70559332	K562	blood:	n/a	n/a
22	POLR2A	chr16:70558857-70559215	GM12891	blood:	n/a	n/a
23	POLR2A	chr16:70559064-70559515	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr16:70558701-70559735	GM12878	blood:	n/a	n/a
25	POLR2A	chr16:70558820-70559358	K562	blood:	n/a	n/a
26	POLR2A	chr16:70556018-70559879	GM12892	blood:	n/a	n/a
27	POLR2A	chr16:70558973-70559594	HepG2	liver:	n/a	n/a
28	POLR2A	chr16:70558799-70559208	GM12878	blood:	n/a	n/a
29	POLR2A	chr16:70558985-70559164	GM12878	blood:	n/a	n/a
30	POLR2A	chr16:70558998-70559530	K562	blood:	n/a	n/a
31	POLR2A	chr16:70558729-70559407	K562	blood:	n/a	n/a
32	TAF1	chr16:70558872-70559221	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr16:70558860-70559564	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr16:70558896-70559274	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr16:70558802-70559226	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr16:70556030-70559733	GM12892	blood:	n/a	n/a
37	POLR2A	chr16:70558659-70559684	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr16:70558738-70559395	K562	blood:	n/a	n/a
39	WRNIP1	chr16:70558897-70559502	GM12878	blood:	n/a	n/a
40	POLR2A	chr16:70559046-70559576	Hela-S3	cervix:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:70486101..70489000-chr16:70557661..70559379,2	K562	blood:
2	chr16:70471134..70474092-chr16:70555921..70560516,5	K562	blood:
3	chr16:70321887..70324896-chr16:70556007..70561529,9	K562	blood:
4	chr16:70456594..70459989-chr16:70556737..70559441,3	K562	blood:
5	chr16:70555634..70562342-chr16:70718026..70723686,6	MCF-7	breast:
6	chr16:70469000..70470691-chr16:70558563..70560602,2	K562	blood:
7	chr16:70540803..70547043-chr16:70555255..70559706,8	MCF-7	breast:
8	chr16:70510287..70517781-chr16:70555054..70559513,7	MCF-7	breast:
9	chr16:70557410..70559180-chr16:70574690..70577736,3	MCF-7	breast:
10	chr16:70558865..70562951-chr16:70591784..70595478,3	MCF-7	breast:
11	chr16:70429611..70435094-chr16:70556538..70559513,5	K562	blood:
12	chr16:70284505..70286615-chr16:70556732..70559559,2	MCF-7	breast:
13	chr16:70379447..70384942-chr16:70556059..70561583,7	K562	blood:
14	chr16:70413215..70416772-chr16:70556199..70563150,13	MCF-7	breast:
15	chr16:70557802..70559378-chr16:70727499..70729855,2	MCF-7	breast:
16	chr16:70413177..70417869-chr16:70554702..70561133,15	MCF-7	breast:
17	chr16:70556657..70559301-chr16:70596912..70598548,2	MCF-7	breast:
18	chr16:70321891..70324896-chr16:70556007..70559559,7	K562	blood:
19	chr16:70379064..70380688-chr16:70557670..70559331,2	MCF-7	breast:
20	chr16:70556717..70559166-chr16:70596632..70598995,2	K562	blood:
21	chr16:70556680..70559302-chr16:70779045..70781738,2	MCF-7	breast:
22	chr16:70285239..70287287-chr16:70556700..70559340,2	K562	blood:
23	chr16:70556330..70559172-chr16:70679219..70681139,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNORD111B	TF binding region
SF3B3	TF binding region
COG4	TF binding region
ENSG00000157353	Chromatin interaction
ENSG00000103043	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000189091	Chromatin interaction
ENSG00000261777	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000157368	Chromatin interaction
ENSG00000157350	Chromatin interaction
ENSG00000132613	Chromatin interaction
ENSG00000223496	Chromatin interaction
ENSG00000260156	Chromatin interaction
ENSG00000157349	Chromatin interaction
ENSG00000168872	Chromatin interaction
ENSG00000090861	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10852465	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11075767	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11075768	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11075769	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11075770	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11640374	0.89[EUR][1000 genomes]
rs11641683	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11643344	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11643373	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11643823	0.89[EUR][1000 genomes]
rs11645092	0.89[EUR][1000 genomes]
rs11645214	0.92[EUR][1000 genomes]
rs11645287	0.89[EUR][1000 genomes]
rs11645437	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11645585	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11648402	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11649624	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11865527	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11866400	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12597401	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12909	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12925729	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12931402	0.86[EUR][1000 genomes]
rs12933634	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2168606	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303792	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2303793	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33910368	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34567847	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34890962	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3762171	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4277334	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4284632	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4324119	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4436771	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4513092	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4592653	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6499320	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6499321	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71401814	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7194521	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7195030	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197262	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7197840	0.93[EUR][1000 genomes]
rs7198317	0.92[EUR][1000 genomes]
rs7199859	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7200430	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7201750	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7204583	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722579	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8045651	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8046881	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8049641	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8049786	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8051506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8052031	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8052125	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8053436	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8057610	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8062178	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8063990	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8064013	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9635522	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9929904	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9936225	0.89[EUR][1000 genomes];0.90[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	nsv833272	chr16:70369769-70569723	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs58963621	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs58963621	CLEC18A	cis	Artery Aorta	GTEx
rs58963621	RP11-296I10.6	cis	Nerve Tibial	GTEx
rs58963621	RP11-419C5.2	cis	Skin Sun Exposed Lower leg	GTEx
rs58963621	RP11-296I10.6	cis	Artery Tibial	GTEx
rs58963621	PDXDC2P	cis	Skin Sun Exposed Lower leg	GTEx
rs58963621	RP11-296I10.6	cis	Thyroid	GTEx
rs58963621	CLEC18A	cis	Whole Blood	GTEx
rs58963621	RP11-296I10.6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70556000-70560200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:70556200-70559200	Active TSS	NHDF-Ad	bronchial
3	chr16:70556400-70560400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr16:70556600-70559200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr16:70556600-70559200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr16:70556600-70559200	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr16:70556600-70559200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:70556600-70559200	Active TSS	NHLF	lung
9	chr16:70556600-70559400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr16:70556600-70559600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr16:70556600-70559800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr16:70556600-70560200	Active TSS	GM12878-XiMat	blood
13	chr16:70556600-70560400	Active TSS	K562	blood
14	chr16:70556800-70559200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr16:70556800-70559200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr16:70556800-70559200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr16:70556800-70559200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr16:70556800-70559200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:70556800-70559200	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr16:70556800-70559200	Active TSS	Fetal Kidney	kidney
21	chr16:70556800-70559200	Bivalent/Poised TSS	HepG2	liver
22	chr16:70556800-70559200	Active TSS	HMEC	breast
23	chr16:70556800-70559200	Active TSS	HSMM	muscle
24	chr16:70556800-70559200	Active TSS	NH-A	brain
25	chr16:70556800-70559200	Active TSS	NHEK	skin
26	chr16:70556800-70559400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:70556800-70559400	Active TSS	Colonic Mucosa	Colon
28	chr16:70556800-70559600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr16:70557000-70559200	Active TSS	Hela-S3	cervix
30	chr16:70557000-70559400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr16:70557000-70559400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr16:70557000-70559600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
33	chr16:70557000-70559600	Active TSS	HSMMtube	muscle
34	chr16:70557400-70559200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr16:70558000-70559400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr16:70558000-70559400	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr16:70558200-70561200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
38	chr16:70558400-70559400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr16:70558400-70559400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr16:70558800-70559200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr16:70558800-70559200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr16:70558800-70559200	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr16:70558800-70559200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr16:70558800-70559200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr16:70558800-70559200	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr16:70558800-70559200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr16:70558800-70559200	Flanking Active TSS	Small Intestine	intestine
48	chr16:70558800-70559400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr16:70558800-70559400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr16:70558800-70559400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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