Variant report

Variant	rs16971138
Chromosome Location	chr16:72699565-72699566
allele	C/T
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	SIN3A	chr16:72698196-72699749	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr16:72698210-72699645	GM12878	blood:	n/a	chr16:72698998-72699013 chr16:72698996-72699011
3	GTF2F1	chr16:72698686-72699591	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr16:72697953-72699947	GM12891	blood:	n/a	n/a
5	RFX5	chr16:72697687-72699776	SK-N-SH	brain:	n/a	chr16:72698994-72699009 chr16:72698965-72698979 chr16:72698997-72699012 chr16:72698997-72699012 chr16:72698963-72698977 chr16:72698997-72699012
6	POLR2A	chr16:72698252-72701233	K562	blood:	n/a	n/a
7	GABPA	chr16:72698244-72699666	MCF-7	breast:	n/a	n/a
8	REST	chr16:72697776-72699636	H1-neurons	neurons:	n/a	chr16:72698260-72698269
9	E2F4	chr16:72697828-72699680	MCF10A-Er-Src	breast:	n/a	chr16:72699063-72699070 chr16:72698332-72698339 chr16:72699063-72699070 chr16:72698332-72698339 chr16:72699060-72699074 chr16:72698332-72698339 chr16:72699063-72699070
10	CHD1	chr16:72698501-72699892	GM12878	blood:	n/a	n/a
11	BHLHE40	chr16:72698656-72699744	GM12878	blood:	n/a	n/a
12	POLR2A	chr16:72698337-72699665	Hela-S3	cervix:	n/a	n/a
13	TBP	chr16:72698695-72699620	Hela-S3	cervix:	n/a	n/a
14	MYC	chr16:72698103-72699628	K562	blood:	n/a	n/a
15	RUNX3	chr16:72698593-72699959	GM12878	blood:	n/a	chr16:72699319-72699328 chr16:72699319-72699328
16	HCFC1	chr16:72698127-72699898	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr16:72698112-72699641	PBDE	blood:	n/a	n/a
18	GATA1	chr16:72698526-72699905	PBDE	blood:	n/a	n/a
19	MXI1	chr16:72697544-72700309	SK-N-SH	brain:	n/a	chr16:72698998-72699013 chr16:72698996-72699011
20	POLR2A	chr16:72698021-72699716	IMR90	lung:	n/a	n/a
21	SMC3	chr16:72698623-72699608	GM12878	blood:	n/a	n/a
22	POLR2A	chr16:72698482-72699620	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:72698108-72699887	GM12878	blood:	n/a	n/a
24	POLR2A	chr16:72698333-72699874	K562	blood:	n/a	n/a
25	NFYB	chr16:72699502-72699907	Hela-S3	cervix:	n/a	n/a
26	UBTF	chr16:72698401-72699591	K562	blood:	n/a	n/a
27	SIN3A	chr16:72698325-72699685	GM12878	blood:	n/a	n/a
28	RELA	chr16:72698163-72699691	GM18951	blood:	n/a	n/a
29	IRF1	chr16:72698077-72699891	K562	blood:	n/a	chr16:72698140-72698153 chr16:72698139-72698153 chr16:72698107-72698121 chr16:72699713-72699727 chr16:72699714-72699728

No.	Distal block	Cell Line	Cell type
1	chr16:72699263..72699769-chrX:47089149..47089659,2	Hela-S3	cervix:
2	chr16:72659577..72662381-chr16:72697498..72700901,3	MCF-7	breast:
3	chr16:72697417..72699588-chr16:73081408..73083430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261008	TF binding region
ENSG00000261008	Chromatin interaction
ENSG00000140836	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1429435	0.88[EUR][1000 genomes]
rs3087608	1.00[CEU][hapmap]
rs55798436	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56394277	0.81[EUR][1000 genomes]
rs59374962	0.90[ASN][1000 genomes]
rs59831429	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7190338	0.84[EUR][1000 genomes]
rs7202635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72789392	0.98[ASN][1000 genomes]
rs72789402	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72791103	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72791108	0.81[EUR][1000 genomes]
rs72793276	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047850	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8050315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9927487	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs9934887	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9939154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv530712	chr16:72499171-72744114	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1063049	chr16:72577004-72887111	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv542952	chr16:72577004-72887111	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv1818026	chr16:72633305-72704680	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1059111	chr16:72647569-72751907	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	esv1822094	chr16:72694760-72787961	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv572958	chr16:72696112-72778617	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72697400-72700200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:72697600-72699600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr16:72697600-72699600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr16:72697600-72699600	Active TSS	Fetal Thymus	thymus
5	chr16:72697600-72699600	Active TSS	HSMM	muscle
6	chr16:72697600-72699800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr16:72697600-72699800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:72697600-72699800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr16:72697600-72699800	Active TSS	Muscle Satellite Cultured Cells	--
10	chr16:72697600-72699800	Active TSS	GM12878-XiMat	blood
11	chr16:72697600-72700000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr16:72697600-72700000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr16:72697600-72700000	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr16:72697600-72700000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:72697600-72700000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr16:72697600-72700000	Active TSS	A549	lung
17	chr16:72697600-72700000	Active TSS	NHLF	lung
18	chr16:72697600-72700400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr16:72697600-72700400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr16:72697800-72699600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr16:72697800-72699600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr16:72697800-72699600	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr16:72697800-72699600	Active TSS	HSMMtube	muscle
24	chr16:72697800-72699800	Active TSS	H9 Cell Line	embryonic stem cell
25	chr16:72697800-72699800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:72697800-72699800	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr16:72697800-72699800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr16:72697800-72699800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr16:72697800-72699800	Active TSS	Fetal Intestine Large	intestine
30	chr16:72697800-72699800	Active TSS	Fetal Stomach	stomach
31	chr16:72697800-72699800	Active TSS	Stomach Smooth Muscle	stomach
32	chr16:72697800-72699800	Active TSS	NHDF-Ad	bronchial
33	chr16:72697800-72700000	Active TSS	Fetal Kidney	kidney
34	chr16:72698000-72699600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr16:72698000-72699600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr16:72698000-72699600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:72698000-72699600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr16:72698000-72699600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr16:72698000-72699600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr16:72698000-72699600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr16:72698000-72699600	Active TSS	Aorta	Aorta
42	chr16:72698000-72699600	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr16:72698000-72699600	Active TSS	Psoas Muscle	Psoas
44	chr16:72698000-72699600	Active TSS	Right Ventricle	heart
45	chr16:72698000-72699600	Bivalent/Poised TSS	HepG2	liver
46	chr16:72698000-72699800	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr16:72698000-72699800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr16:72698000-72699800	Active TSS	Fetal Intestine Small	intestine
49	chr16:72698000-72699800	Active TSS	Fetal Muscle Trunk	muscle
50	chr16:72698000-72699800	Active TSS	Ovary	ovary

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