Variant report

Variant	rs1532752
Chromosome Location	chr16:46654670-46654671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr16:46654540-46655458	MCF-7	breast:	n/a	chr16:46655048-46655060
2	MAX	chr16:46654582-46655514	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr16:46654632-46655577	GM18505	blood:	n/a	n/a
4	YY1	chr16:46654626-46655505	GM12878	blood:	n/a	chr16:46654923-46654937
5	SPI1	chr16:46654650-46654943	GM12878	blood:	n/a	chr16:46654785-46654798 chr16:46654785-46654798
6	YY1	chr16:46654637-46655491	SK-N-SH	brain:	n/a	chr16:46654923-46654937
7	POLR2A	chr16:46654634-46655421	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr16:46654628-46655468	Hela-S3	cervix:	n/a	n/a
9	SPI1	chr16:46654634-46654950	K562	blood:	n/a	chr16:46654785-46654798 chr16:46654785-46654798
10	YY1	chr16:46654590-46655560	ECC-1	luminal epithelium:	n/a	chr16:46654923-46654937
11	YY1	chr16:46654586-46655467	H1-hESC	embryonic stem cell:	n/a	chr16:46654923-46654937
12	POLR2A	chr16:46654599-46655426	K562	blood:	n/a	n/a
13	YY1	chr16:46654626-46655493	H1-hESC	embryonic stem cell:	n/a	chr16:46654923-46654937
14	POLR2A	chr16:46654635-46655462	K562	blood:	n/a	n/a
15	YY1	chr16:46654626-46655460	GM12878	blood:	n/a	chr16:46654923-46654937
16	POLR2A	chr16:46654608-46655574	GM18526	blood:	n/a	n/a
17	YY1	chr16:46654626-46655430	K562	blood:	n/a	chr16:46654923-46654937
18	POLR2A	chr16:46654585-46655503	H1-hESC	embryonic stem cell:	n/a	n/a
19	SPI1	chr16:46654145-46655108	HL-60	blood:	n/a	chr16:46654785-46654798 chr16:46654785-46654798
20	MXI1	chr16:46654213-46655888	SK-N-SH	brain:	n/a	chr16:46655288-46655303
21	CREB1	chr16:46654619-46655580	HepG2	liver:	n/a	chr16:46654716-46654729
22	POLR2A	chr16:46654567-46655483	HL-60	blood:	n/a	n/a
23	SIN3A	chr16:46654536-46655548	H1-hESC	embryonic stem cell:	n/a	chr16:46655281-46655294 chr16:46655058-46655068
24	MAX	chr16:46654299-46655472	NB4	blood:	n/a	n/a
25	POLR2A	chr16:46654576-46655530	GM19099	blood:	n/a	n/a
26	YY1	chr16:46654657-46655488	GM12892	blood:	n/a	chr16:46654923-46654937
27	YY1	chr16:46654588-46655497	A549	lung:	n/a	chr16:46654923-46654937
28	CREB1	chr16:46654625-46655585	HepG2	liver:	n/a	chr16:46654716-46654729
29	REST	chr16:46654553-46655478	HL-60	blood:	n/a	chr16:46655058-46655067
30	SPI1	chr16:46654640-46654889	GM12891	blood:	n/a	chr16:46654785-46654798 chr16:46654785-46654798
31	MXI1	chr16:46654170-46655948	IMR90	lung:	n/a	chr16:46655288-46655303
32	POLR2A	chr16:46654462-46655540	HL-60	blood:	n/a	n/a
33	SPI1	chr16:46654594-46655033	HL-60	blood:	n/a	chr16:46654785-46654798 chr16:46654785-46654798
34	POLR2A	chr16:46654650-46655553	GM12892	blood:	n/a	n/a
35	YY1	chr16:46654640-46655478	ECC-1	luminal epithelium:	n/a	chr16:46654923-46654937
36	POLR2A	chr16:46654629-46655611	GM12891	blood:	n/a	n/a
37	SPI1	chr16:46654647-46654907	K562	blood:	n/a	chr16:46654785-46654798 chr16:46654785-46654798
38	TAF1	chr16:46654635-46655665	ECC-1	luminal epithelium:	n/a	n/a
39	TAF1	chr16:46654606-46655483	H1-hESC	embryonic stem cell:	n/a	n/a
40	YY1	chr16:46654645-46655445	HepG2	liver:	n/a	chr16:46654923-46654937
41	MAX	chr16:46654626-46655513	K562	blood:	n/a	n/a
42	E2F4	chr16:46653976-46655954	MCF10A-Er-Src	breast:	n/a	chr16:46655048-46655060
43	HCFC1	chr16:46654433-46655823	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:46651769..46655217-chr16:46661271..46664188,4	K562	blood:
2	chr16:46649901..46653063-chr16:46653348..46656157,4	K562	blood:
3	chr16:46653721..46656886-chr16:46721851..46724551,4	K562	blood:
4	chr16:46589331..46591714-chr16:46654314..46656100,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS35-1	chr16:46654378-46654812	NONHSAT142254

Variant related genes	Relation type
SHCBP1	TF binding region
ENSG00000171241	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000069329	Chromatin interaction
ENSG00000199448	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1054722	0.82[YRI][hapmap]
rs12447101	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1369935	0.81[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1436437	1.00[MKK][hapmap];0.85[YRI][hapmap]
rs1436438	0.83[YRI][hapmap]
rs1992077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4405571	0.82[YRI][hapmap]
rs4966442	0.81[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap]
rs4966532	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4967156	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4967247	0.82[YRI][hapmap]
rs7191748	0.81[LWK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs7197337	0.81[LWK][hapmap];1.00[MKK][hapmap]
rs794562	0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8050258	0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8052092	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8059337	0.94[YRI][hapmap]
rs9935497	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799780	chr16:46386457-46875496	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv1848852	chr16:46463746-46659554	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv917899	chr16:46463769-46669332	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1056162	chr16:46463770-46655516	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1066221	chr16:46463770-46699143	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1060734	chr16:46463770-46768102	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1064289	chr16:46463770-46801977	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
9	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	esv1806429	chr16:46468179-46659554	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	esv1847767	chr16:46474763-46659354	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	esv1815153	chr16:46474763-46672206	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
13	esv1797185	chr16:46489836-46731413	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv1066048	chr16:46500740-46998694	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv542908	chr16:46500740-46998694	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
17	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
18	nsv833216	chr16:46501297-46671860	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
19	nsv916976	chr16:46505597-46801868	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
20	nsv526656	chr16:46539392-46846663	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv428327	chr16:46556968-46718490	Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:46632200-46654800	Weak transcription	Pancreas	Pancrea
2	chr16:46646600-46654800	Weak transcription	Aorta	Aorta
3	chr16:46647200-46654800	Weak transcription	Spleen	Spleen
4	chr16:46650600-46654800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr16:46653600-46655600	Active TSS	GM12878-XiMat	blood
6	chr16:46654000-46654800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr16:46654000-46654800	Flanking Active TSS	HMEC	breast
8	chr16:46654000-46655000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr16:46654000-46655400	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr16:46654000-46655400	Active TSS	NH-A	brain
11	chr16:46654000-46655600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr16:46654000-46655600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr16:46654000-46655600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr16:46654000-46655600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:46654000-46655600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:46654000-46655600	Active TSS	A549	lung
17	chr16:46654000-46655600	Active TSS	NHDF-Ad	bronchial
18	chr16:46654000-46655800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr16:46654200-46654800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr16:46654200-46654800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr16:46654200-46654800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr16:46654200-46654800	Flanking Active TSS	NHEK	skin
23	chr16:46654200-46655000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr16:46654200-46655000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:46654200-46655000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr16:46654200-46655000	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr16:46654200-46655000	Flanking Active TSS	Thymus	Thymus
28	chr16:46654200-46655200	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr16:46654200-46655400	Active TSS	HSMM	muscle
30	chr16:46654200-46655600	Active TSS	H1 Cell Line	embryonic stem cell
31	chr16:46654200-46655600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr16:46654200-46655600	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr16:46654200-46655600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr16:46654200-46655800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr16:46654400-46654800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr16:46654400-46654800	Flanking Active TSS	Fetal Lung	lung
37	chr16:46654400-46654800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr16:46654400-46655000	Flanking Active TSS	Primary B cells from peripheral blood	blood
39	chr16:46654400-46655000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr16:46654400-46655000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr16:46654400-46655000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr16:46654400-46655000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr16:46654400-46655000	Flanking Active TSS	Fetal Stomach	stomach
44	chr16:46654400-46655000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr16:46654400-46655200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr16:46654400-46655400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:46654400-46655400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr16:46654400-46655400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr16:46654400-46655400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr16:46654400-46655400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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