Variant report

Variant	rs17608557
Chromosome Location	chr16:72459517-72459518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:72459512-72459616	MCF-7	breast:	n/a	n/a
2	POLR2A	chr16:72459480-72459801	Gliobla	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:72459516-72459566	HAEpiC	amniotic membrane:	n/a
2	chr16:72459516-72459566	HCT-116	colon:	n/a
3	chr16:72459516-72459566	SK-N-MC	brain:	n/a
4	chr16:72459516-72459566	ovcar-3	ovarian:	n/a
5	chr16:72459516-72459566	MCF-7	breast:	n/a
6	chr16:72459516-72459566	SKMC	muscle:	n/a
7	chr16:72459516-72459566	PFSK-1	brain:	n/a
8	chr16:72459516-72459566	NHBE	bronchial:	n/a
9	chr16:72459516-72459566	NH-A	brain:	n/a
10	chr16:72459516-72459566	U87	brain:	n/a
11	chr16:72459516-72459566	GM12892	blood:	n/a
12	chr16:72459516-72459566	T-47D	breast:	n/a
13	chr16:72459516-72459566	HRCEpiC	kidney:	n/a
14	chr16:72459516-72459566	ECC-1	luminal epithelium:	n/a
15	chr16:72459516-72459566	HPAEpiC	pulmonary alveolar:	n/a
16	chr16:72459516-72459566	GM06990	blood:	n/a
17	chr16:72459516-72459566	HRE	kidney:	n/a
18	chr16:72459516-72459566	HNPCEpiC	eye:	n/a
19	chr16:72459516-72459566	CMK	blood:	n/a
20	chr16:72459516-72459566	BJ	skin:	n/a
21	chr16:72459516-72459566	HEK293	kidney:	embryo
22	chr16:72459516-72459566	SK-N-SH	brain:	n/a
23	chr16:72459516-72459566	NHDF-neo	bronchial:	n/a
24	chr16:72459516-72459566	SK-N-SH_RA	brain:	n/a
25	chr16:72459516-72459566	Jurkat	blood:	n/a
26	chr16:72459516-72459566	ProgFib	skin:	n/a
27	chr16:72459516-72459566	HCPEpiC	choroid plexus:	n/a
28	chr16:72459516-72459566	RPTEC	kidney:	n/a
29	chr16:72459516-72459566	PANC-1	pancreas:	n/a
30	chr16:72459516-72459566	Hepatocyte	liver:	n/a
31	chr16:72459516-72459566	BE2_C	brain:	n/a
32	chr16:72459516-72459566	GM19239	blood:	n/a
33	chr16:72459516-72459566	Hela-S3	cervix:	n/a
34	chr16:72459516-72459566	PrEC	prostate:	n/a
35	chr16:72459516-72459566	NT2-D1	testis:	n/a
36	chr16:72459516-72459566	HRPEpiC	eye:	n/a
37	chr16:72459516-72459566	AG09319	gingival:	n/a
38	chr16:72459516-72459566	AG04450	lung:	fetal
39	chr16:72459516-72459566	AoSMC	blood vessel:	n/a
40	chr16:72459516-72459566	HepG2	liver:	n/a
41	chr16:72459516-72459566	MCF10A-Er-Src	breast:	n/a
42	chr16:72459516-72459566	NB4	blood:	n/a
43	chr16:72459516-72459566	HUVEC	blood vessel:	n/a
44	chr16:72459516-72459566	AG04449	skin:	fetal
45	chr16:72459516-72459566	HL-60	blood:	n/a
46	chr16:72459516-72459566	GM12878	blood:	n/a
47	chr16:72459516-72459566	GM12891	blood:	n/a
48	chr16:72459516-72459566	SAEC	small airway:	n/a
49	chr16:72459516-72459566	AG09309	skin:	n/a
50	chr16:72459516-72459566	HIPEpiC	eye:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PMFBP1-4	chr16:72459384-72461356	ENSG00000261008.2

No data

Variant related genes	Relation type
ENSG00000260664	TF binding region
ENSG00000260664	CpG island

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10468266	0.82[AMR][1000 genomes]
rs10492821	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10492822	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11643203	0.85[AMR][1000 genomes]
rs12325146	0.80[ASN][1000 genomes]
rs12325151	0.80[ASN][1000 genomes]
rs13333122	0.83[CEU][hapmap]
rs1429071	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16970933	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971030	0.82[AMR][1000 genomes]
rs16971036	0.82[AMR][1000 genomes]
rs16971037	0.82[AMR][1000 genomes]
rs16971050	0.86[AMR][1000 genomes]
rs17608394	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17609544	0.80[ASN][1000 genomes]
rs17609577	0.80[ASN][1000 genomes]
rs17676691	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17676709	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17677146	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17677484	0.80[ASN][1000 genomes]
rs17677616	0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2163068	0.82[AMR][1000 genomes]
rs2336437	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55766519	0.86[AMR][1000 genomes]
rs56347149	0.82[AMR][1000 genomes]
rs56348767	0.82[AMR][1000 genomes]
rs56389222	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57755001	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs58770834	0.82[AMR][1000 genomes]
rs58860566	0.81[AFR][1000 genomes]
rs59966262	0.80[ASN][1000 genomes]
rs60502114	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs62051129	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62051130	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62051131	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62051136	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62051137	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62051145	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62051146	0.84[AMR][1000 genomes]
rs62051147	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62051148	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62051149	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62051150	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62051151	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62052871	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs62052877	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62052878	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62052879	0.82[AMR][1000 genomes]
rs62052895	0.81[AFR][1000 genomes]
rs62052915	0.84[AMR][1000 genomes]
rs62052920	0.82[AMR][1000 genomes]
rs62052921	0.82[AMR][1000 genomes]
rs62052927	0.82[AMR][1000 genomes]
rs62052954	0.82[AMR][1000 genomes]
rs62053991	0.81[ASN][1000 genomes]
rs62054469	0.85[AMR][1000 genomes]
rs62054470	0.85[AMR][1000 genomes]
rs7192221	0.82[AMR][1000 genomes]
rs7194024	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7195825	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7198449	0.81[ASN][1000 genomes]
rs7198788	0.82[AMR][1000 genomes]
rs7199954	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7199970	0.82[AMR][1000 genomes]
rs7205109	0.83[CEU][hapmap]
rs7206298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72791149	0.80[ASN][1000 genomes]
rs72793244	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72793252	0.85[AMR][1000 genomes]
rs72793263	0.82[AMR][1000 genomes]
rs72793266	0.82[AMR][1000 genomes]
rs72793271	0.82[AMR][1000 genomes]
rs806732	0.80[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs806733	0.88[JPT][hapmap]
rs806738	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs999697	0.82[AMR][1000 genomes]
rs999698	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1063172	chr16:72342110-72537808	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv542947	chr16:72342110-72537808	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1057127	chr16:72375524-72509686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv542949	chr16:72375524-72509686	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv572956	chr16:72426448-72517014	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72443600-72461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:72451400-72459600	Weak transcription	Primary B cells from cord blood	blood
3	chr16:72455200-72462600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:72457000-72461600	Weak transcription	HepG2	liver
5	chr16:72457200-72467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:72457600-72460400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:72457800-72461200	Weak transcription	Fetal Intestine Small	intestine
8	chr16:72457800-72461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr16:72457800-72462800	Weak transcription	Primary T cells from cord blood	blood
10	chr16:72458000-72459600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr16:72458000-72461400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr16:72458200-72459800	Weak transcription	Fetal Intestine Large	intestine
13	chr16:72458600-72459600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr16:72458600-72459600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr16:72458600-72460600	Active TSS	NH-A	brain
16	chr16:72458600-72461600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr16:72458600-72463400	Active TSS	Fetal Brain Female	brain
18	chr16:72458600-72464800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr16:72458600-72465400	Active TSS	Brain Substantia Nigra	brain
20	chr16:72458600-72465600	Active TSS	Brain Anterior Caudate	brain
21	chr16:72458600-72465800	Active TSS	Brain Angular Gyrus	brain
22	chr16:72458600-72465800	Active TSS	Brain Cingulate Gyrus	brain
23	chr16:72458800-72460400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr16:72458800-72460400	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr16:72458800-72460600	Strong transcription	Dnd41	blood
26	chr16:72458800-72461400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr16:72458800-72462000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr16:72458800-72462400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr16:72458800-72463200	Active TSS	Brain Germinal Matrix	brain
30	chr16:72458800-72466000	Active TSS	Brain Hippocampus Middle	brain
31	chr16:72459000-72460000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr16:72459000-72460600	Active TSS	Fetal Brain Male	brain
33	chr16:72459000-72464000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr16:72459000-72464800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:72459200-72460000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr16:72459400-72459600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr16:72459400-72460000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr16:72459400-72460000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr16:72459400-72460200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr16:72459400-72460200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:72459400-72460200	ZNF genes & repeats	Fetal Stomach	stomach
42	chr16:72459400-72460200	Strong transcription	Thymus	Thymus

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