Variant report

Variant	rs16960903
Chromosome Location	chr17:63181941-63181942
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:57)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:57 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:63181860-63182010	HMF	breast:	n/a	n/a
2	CTCF	chr17:63181820-63181970	GM12872	blood:	n/a	n/a
3	CTCF	chr17:63181900-63182050	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr17:63181900-63182050	GM12873	blood:	n/a	n/a
5	CTCF	chr17:63181840-63181990	GM12869	blood:	n/a	n/a
6	CTCF	chr17:63181840-63181990	Caco-2	colon:	n/a	n/a
7	CTCF	chr17:63181920-63182070	HCM	heart:	n/a	n/a
8	EP300	chr17:63179682-63182280	SK-N-SH	brain:	n/a	chr17:63180252-63180266 chr17:63180019-63180029
9	CTCF	chr17:63181900-63182050	GM12875	blood:	n/a	n/a
10	CTCF	chr17:63181880-63182030	GM12878	blood:	n/a	n/a
11	CTCF	chr17:63181860-63182010	HCT-116	colon:	n/a	n/a
12	GATA2	chr17:63181079-63182143	SH-SY5Y	brain:	n/a	n/a
13	CTCF	chr17:63181830-63182230	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr17:63181779-63182074	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr17:63181699-63182143	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr17:63181900-63182050	MCF-7	breast:	n/a	n/a
17	CTCF	chr17:63181920-63182070	HUVEC	blood vessel:	n/a	n/a
18	CTCF	chr17:63181900-63182050	GM12864	blood:	n/a	n/a
19	CTCF	chr17:63181920-63182070	GM12872	blood:	n/a	n/a
20	CTCF	chr17:63181940-63182090	HepG2	liver:	n/a	n/a
21	CTCF	chr17:63181820-63181970	NB4	blood:	n/a	n/a
22	CTCF	chr17:63181896-63182161	K562	blood:	n/a	n/a
23	YY1	chr17:63181852-63182131	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr17:63181920-63182070	BE2_C	brain:	n/a	n/a
25	CTCF	chr17:63181860-63182010	HPAF	blood vessel:	n/a	n/a
26	CTCF	chr17:63181860-63182010	GM12865	blood:	n/a	n/a
27	CTCF	chr17:63181900-63182037	SK-N-SH_RA	brain:	n/a	n/a
28	CTCF	chr17:63181860-63182010	BE2_C	brain:	n/a	n/a
29	CTCF	chr17:63181840-63182110	AG04450	lung:	n/a	n/a
30	CTCF	chr17:63181820-63181970	GM06990	blood:	n/a	n/a
31	RAD21	chr17:63181807-63182167	SK-N-SH_RA	brain:	n/a	n/a
32	CTCF	chr17:63181900-63182050	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr17:63181840-63181990	GM12878	blood:	n/a	n/a
34	POLR2A	chr17:63181722-63182256	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr17:63181800-63181950	A549	lung:	n/a	n/a
36	CTCF	chr17:63181884-63182071	K562	blood:	n/a	n/a
37	CTCF	chr17:63181920-63182070	HPAF	blood vessel:	n/a	n/a
38	CTCF	chr17:63181765-63182112	K562	blood:	n/a	n/a
39	CTCF	chr17:63181860-63182010	RPTEC	kidney:	n/a	n/a
40	CTCF	chr17:63181860-63182010	SK-N-SH_RA	brain:	n/a	n/a
41	RAD21	chr17:63181797-63182104	SK-N-SH_RA	brain:	n/a	n/a
42	CTCF	chr17:63181897-63182120	K562	blood:	n/a	n/a
43	CTCF	chr17:63181880-63182030	HEK293	kidney:	n/a	n/a
44	CTCF	chr17:63181840-63181990	GM12873	blood:	n/a	n/a
45	CTCF	chr17:63181900-63182050	K562	blood:	n/a	n/a
46	CTCF	chr17:63181860-63182010	GM12866	blood:	n/a	n/a
47	CTCF	chr17:63181900-63182050	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr17:63181880-63182030	A549	lung:	n/a	n/a
49	CTCF	chr17:63181860-63182010	HEK293	kidney:	n/a	n/a
50	CTCF	chr17:63181840-63181990	HCPEpiC	choroid plexus:	n/a	n/a

No data

Variant related genes	Relation type
RGS9	TF binding region
ENSG00000265883	TF binding region

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10514867	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11650746	0.94[ASN][1000 genomes]
rs11651062	0.94[ASN][1000 genomes]
rs11651081	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654243	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654391	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11657250	0.94[ASN][1000 genomes]
rs11658655	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11658673	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658736	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658773	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16960905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960957	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16961015	1.00[CHB][hapmap]
rs16961273	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28451574	0.81[ASN][1000 genomes]
rs28525077	0.81[ASN][1000 genomes]
rs2869578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869579	0.94[ASN][1000 genomes]
rs2869580	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2869582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2869584	0.94[ASN][1000 genomes]
rs4293415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588019	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4791220	0.89[CEU][hapmap]
rs4791223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791228	0.80[EUR][1000 genomes]
rs55948632	0.81[ASN][1000 genomes]
rs55948933	0.94[ASN][1000 genomes]
rs56102951	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59173947	0.81[ASN][1000 genomes]
rs61708414	0.81[ASN][1000 genomes]
rs7207726	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs7211341	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215502	0.94[ASN][1000 genomes]
rs7217524	1.00[JPT][hapmap]
rs7217548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7218518	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7220710	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7220949	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7221103	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73330407	0.87[ASN][1000 genomes]
rs73347632	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8065444	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8065725	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8066063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8066072	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8068016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8071603	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8072543	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8080929	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs908089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9889653	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9896245	1.00[CEU][hapmap]
rs9897592	1.00[CEU][hapmap]
rs9898825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9900568	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9900709	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9901108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9904207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9907146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9907374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9908359	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9914418	0.94[ASN][1000 genomes]
rs9914790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9916092	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9916789	0.94[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	nsv530764	chr17:62939944-63278472	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16960903	YPEL2	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:63169800-63190800	Weak transcription	Gastric	stomach
2	chr17:63176400-63223800	Weak transcription	Lung	lung
3	chr17:63178800-63182000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr17:63178800-63182200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:63179000-63183000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:63179200-63182000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:63179400-63182200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr17:63179400-63182600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr17:63179600-63182200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:63179600-63182200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:63179600-63182200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr17:63179600-63182200	Enhancers	Fetal Brain Male	brain
13	chr17:63179600-63183000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:63179800-63182200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:63179800-63182200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:63179800-63182200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:63180000-63194600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:63180400-63182200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr17:63180400-63182200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:63180600-63182000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:63180600-63182000	Enhancers	A549	lung
22	chr17:63180600-63182200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr17:63180600-63182200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr17:63180600-63182200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr17:63180600-63186800	Weak transcription	Colon Smooth Muscle	Colon
26	chr17:63180600-63194800	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:63180800-63182000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr17:63180800-63186600	Weak transcription	Brain Anterior Caudate	brain
29	chr17:63181000-63182200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr17:63181200-63187400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr17:63181200-63192800	Weak transcription	Dnd41	blood
32	chr17:63181200-63197400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr17:63181400-63182200	Enhancers	Fetal Stomach	stomach
34	chr17:63181400-63184400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr17:63181600-63183000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr17:63181600-63186800	Weak transcription	HSMMtube	muscle
37	chr17:63181600-63189400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:63181800-63209600	Weak transcription	Rectal Smooth Muscle	rectum

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