Variant report

Variant	rs17552310
Chromosome Location	chr17:16341867-16341868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:500)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:500 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr17:16341735-16342765	H1-hESC	embryonic stem cell:	n/a	chr17:16341993-16342004
2	USF1	chr17:16341593-16342388	A549	lung:	n/a	chr17:16341993-16342004
3	HA-E2F1	chr17:16341734-16342944	MCF-7	breast:	n/a	chr17:16342132-16342141
4	YY1	chr17:16341675-16342523	H1-hESC	embryonic stem cell:	n/a	n/a
5	MTA3	chr17:16341470-16343759	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:16341507-16344039	GM18505	blood:	n/a	n/a
7	SIN3A	chr17:16341696-16343827	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr17:16341773-16342404	HepG2	liver:	n/a	n/a
9	GTF2F1	chr17:16341760-16343526	K562	blood:	n/a	n/a
10	POLR2A	chr17:16341731-16343941	HepG2	liver:	n/a	n/a
11	KAT2A	chr17:16341666-16343615	Hela-S3	cervix:	n/a	n/a
12	MBD4	chr17:16341588-16343970	HepG2	liver:	n/a	n/a
13	YY1	chr17:16341759-16342476	NT2-D1	testis:	n/a	n/a
14	REST	chr17:16341672-16342749	HL-60	blood:	n/a	chr17:16341690-16341703
15	ELF1	chr17:16341744-16342684	A549	lung:	n/a	n/a
16	POLR2A	chr17:16341287-16348457	GM12892	blood:	n/a	n/a
17	POLR2A	chr17:16341231-16355258	PFSK-1	brain:	n/a	n/a
18	CEBPB	chr17:16341695-16342339	A549	lung:	n/a	chr17:16341880-16341891 chr17:16341879-16341892 chr17:16341904-16341915
19	POLR2A	chr17:16341181-16348546	GM12892	blood:	n/a	n/a
20	RCOR1	chr17:16341727-16342662	HepG2	liver:	n/a	n/a
21	MXI1	chr17:16341705-16343204	H1-hESC	embryonic stem cell:	n/a	n/a
22	HCFC1	chr17:16341556-16342633	K562	blood:	n/a	n/a
23	MAX	chr17:16341720-16343860	Hela-S3	cervix:	n/a	n/a
24	IRF3	chr17:16341865-16342380	GM12878	blood:	n/a	n/a
25	TAF1	chr17:16341605-16342610	Hela-S3	cervix:	n/a	n/a
26	USF1	chr17:16341738-16342316	H1-hESC	embryonic stem cell:	n/a	chr17:16341993-16342004
27	EP300	chr17:16341829-16342481	SK-N-SH_RA	brain:	n/a	chr17:16341877-16341891
28	MYC	chr17:16341795-16342425	MCF-7	breast:	n/a	n/a
29	IRF4	chr17:16341754-16342533	GM12878	blood:	n/a	n/a
30	TCF7L2	chr17:16341683-16342816	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr17:16341461-16343264	A549	lung:	n/a	n/a
32	NFIC	chr17:16341597-16342701	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr17:16341581-16343921	GM15510	blood:	n/a	n/a
34	EP300	chr17:16341781-16342433	GM12878	blood:	n/a	chr17:16341877-16341891
35	FOXA1	chr17:16341780-16342573	HepG2	liver:	n/a	n/a
36	SP1	chr17:16341610-16342533	HepG2	liver:	n/a	chr17:16342098-16342109
37	POU2F2	chr17:16341782-16342091	GM12878	blood:	n/a	n/a
38	TAF1	chr17:16341744-16342059	GM12878	blood:	n/a	n/a
39	USF1	chr17:16341435-16342659	HCT-116	colon:	n/a	chr17:16341993-16342004
40	POU2F2	chr17:16341470-16342640	GM12878	blood:	n/a	n/a
41	USF2	chr17:16341628-16342524	GM12878	blood:	n/a	chr17:16341993-16342004
42	FOSL2	chr17:16341527-16342540	A549	lung:	n/a	n/a
43	POLR2A	chr17:16341449-16348238	GM12878	blood:	n/a	n/a
44	MAFK	chr17:16341826-16342948	K562	blood:	n/a	n/a
45	CEBPD	chr17:16341708-16342029	HepG2	liver:	n/a	n/a
46	YY1	chr17:16341775-16342525	K562	blood:	n/a	n/a
47	CHD2	chr17:16341631-16343719	K562	blood:	n/a	n/a
48	MYC	chr17:16341720-16342569	MCF10A-Er-Src	breast:	n/a	n/a
49	SP1	chr17:16341678-16342558	H1-hESC	embryonic stem cell:	n/a	chr17:16342098-16342109
50	POLR2A	chr17:16341378-16344127	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:113217131..113217743-chr17:16341573..16342194,2	Hela-S3	cervix:
2	chr17:16341411..16344243-chr17:16555470..16557634,2	K562	blood:
3	chr17:16340606..16343390-chr17:16393092..16395708,2	MCF-7	breast:
4	chr17:16341453..16342412-chr2:64067490..64068202,2	NB4	blood:
5	chr17:16325375..16336653-chr17:16340697..16345018,16	MCF-7	breast:
6	chr17:16282507..16286910-chr17:16340967..16348886,17	K562	blood:
7	chr1:149223735..149225303-chr17:16340885..16343606,2	MCF-7	breast:
8	chr17:16341750..16342479-chr19:45681510..45682384,2	Hela-S3	cervix:
9	chr17:16341531..16342406-chr17:73150204..73150815,2	Hela-S3	cervix:
10	chr11:9684969..9685654-chr17:16341865..16342578,2	Hela-S3	cervix:
11	chr17:16282813..16296019-chr17:16339657..16347255,30	K562	blood:
12	chr17:16341089..16343780-chr19:1248393..1250023,2	MCF-7	breast:
13	chr17:16317117..16319974-chr17:16340448..16343551,4	MCF-7	breast:
14	chr17:16117937..16120860-chr17:16340907..16344654,4	K562	blood:
15	chr17:16327763..16335480-chr17:16339357..16343915,19	MCF-7	breast:
16	chr17:16316817..16323346-chr17:16340136..16347615,14	MCF-7	breast:
17	chr17:16280844..16288183-chr17:16338320..16344372,17	MCF-7	breast:
18	chr17:16118917..16121426-chr17:16341120..16343503,3	MCF-7	breast:
19	chr10:74032655..74033340-chr17:16341554..16342084,2	Hela-S3	cervix:
20	chr17:16282005..16293050-chr17:16338399..16351573,30	MCF-7	breast:
21	chr17:16189460..16191732-chr17:16340312..16341951,2	K562	blood:
22	chr17:16254878..16257710-chr17:16340945..16342947,3	K562	blood:
23	chr17:16321222..16324039-chr17:16340513..16343570,3	MCF-7	breast:

No data

Variant related genes	Relation type
FAM211A-AS1	TF binding region
ENSG00000108474	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000141027	Chromatin interaction
ENSG00000181350	Chromatin interaction
ENSG00000170315	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000133789	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000265095	Chromatin interaction
ENSG00000166582	Chromatin interaction
ENSG00000239203	Chromatin interaction
ENSG00000264739	Chromatin interaction
ENSG00000187688	Chromatin interaction
ENSG00000189159	Chromatin interaction
ENSG00000197566	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000264765	Chromatin interaction
ENSG00000265401	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11078342	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11078343	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11078344	0.81[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11078345	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11653149	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11654069	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11867498	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11869614	0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11870279	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11871017	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11871929	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11871958	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11871963	0.96[GIH][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12936240	1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12938294	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12940078	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17715447	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34166276	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34192401	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34419652	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34572942	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34577506	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34779276	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34793697	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34982046	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35034622	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35247166	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35269706	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35377488	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35474528	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35540454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35774281	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36117589	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56097826	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7217211	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs941411	0.90[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1065254	chr17:16252880-16389930	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
9	nsv428668	chr17:16265210-16455285	Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17552310	TRPV2	cis	parietal	SCAN
rs17552310	C17orf45	Cis_1M	lymphoblastoid	RTeQTL
rs17552310	SNORD49B	cis	cerebellum	SCAN
rs17552310	SNORD49B	cis	parietal	SCAN
rs17552310	SNORD49A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16341200-16342000	Flanking Active TSS	Dnd41	blood
2	chr17:16341400-16342000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr17:16341400-16342000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr17:16341400-16342000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr17:16341400-16342000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:16341400-16342000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr17:16341400-16342000	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr17:16341400-16342000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr17:16341400-16342000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr17:16341400-16342000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:16341400-16342000	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr17:16341400-16342000	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr17:16341400-16342000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr17:16341400-16342000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr17:16341400-16342000	Flanking Active TSS	GM12878-XiMat	blood
16	chr17:16341400-16342000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr17:16341400-16342000	Flanking Active TSS	NHEK	skin
18	chr17:16341400-16342000	Flanking Active TSS	NHLF	lung
19	chr17:16341400-16342000	Flanking Active TSS	Osteobl	bone
20	chr17:16341400-16342400	Active TSS	Fetal Brain Female	brain
21	chr17:16341400-16342800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr17:16341400-16343000	Active TSS	H1 Cell Line	embryonic stem cell
23	chr17:16341400-16343000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:16341400-16343000	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr17:16341400-16343000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr17:16341400-16343200	Active TSS	Brain Anterior Caudate	brain
27	chr17:16341400-16343200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:16341400-16343400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:16341400-16344400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:16341600-16342000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:16341600-16342000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:16341600-16342000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr17:16341600-16342000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr17:16341600-16342000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:16341600-16342000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr17:16341600-16342000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr17:16341600-16342000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr17:16341600-16342000	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr17:16341600-16342000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr17:16341600-16342000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr17:16341600-16342000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr17:16341600-16342000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr17:16341600-16342000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:16341600-16342000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:16341600-16342000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr17:16341600-16342000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr17:16341600-16342000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:16341600-16342000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr17:16341600-16342000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr17:16341600-16342000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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