Variant report

Variant	rs3759933
Chromosome Location	chr16:81042004-81042005
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81039828-81042424	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr16:81041854-81042190	K562	blood:	n/a	n/a
3	POLR2A	chr16:81042001-81042148	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:81039833-81042011	GM12892	blood:	n/a	n/a
5	JUND	chr16:81039279-81042090	SK-N-SH	brain:	n/a	chr16:81041079-81041088
6	YY1	chr16:81041879-81042119	K562	blood:	n/a	n/a
7	POLR2A	chr16:81039798-81042062	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:81039886-81042074	HepG2	liver:	n/a	n/a
9	YY1	chr16:81041801-81042164	GM12892	blood:	n/a	n/a
10	MXI1	chr16:81039145-81042276	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr16:81041938-81042428	K562	blood:	n/a	n/a
12	POLR2A	chr16:81039896-81042204	K562	blood:	n/a	n/a
13	HCFC1	chr16:81039075-81042051	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr16:81040075-81042015	HUVEC	blood vessel:	n/a	n/a
15	HEY1	chr16:81039788-81042481	K562	blood:	n/a	chr16:81041078-81041087 chr16:81041080-81041089 chr16:81040141-81040156
16	CHD1	chr16:81039191-81042059	IMR90	lung:	n/a	chr16:81041086-81041096
17	SREBP1	chr16:81040019-81042204	GM12878	blood:	n/a	n/a
18	POLR2A	chr16:81039866-81042151	GM12878	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81038105..81044923-chr16:81066300..81070952,14	MCF-7	breast:
2	chr16:81037151..81044642-chr16:81065528..81070966,16	K562	blood:
3	chr16:81028135..81034571-chr16:81035246..81044200,13	K562	blood:
4	chr16:81041195..81043278-chr16:81298968..81300787,2	MCF-7	breast:
5	chr16:81041193..81042878-chr16:81061332..81063223,2	MCF-7	breast:
6	chr16:81037996..81043724-chr16:81066407..81071400,11	MCF-7	breast:
7	chr16:81038376..81042418-chr16:81108432..81111584,4	K562	blood:
8	chr16:81037094..81043910-chr16:81050858..81058489,11	MCF-7	breast:
9	chr16:81041089..81043936-chr16:81047527..81050670,4	MCF-7	breast:
10	chr16:81038376..81043277-chr16:81108432..81112403,6	K562	blood:
11	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
12	chr16:81006720..81008991-chr16:81041065..81043268,2	MCF-7	breast:
13	chr16:81041904..81044341-chr16:81779163..81781549,2	MCF-7	breast:
14	chr16:81039722..81044457-chr16:81106699..81112118,5	MCF-7	breast:

No data

Variant related genes	Relation type
CMC2	TF binding region
ENSG00000103121	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000245059	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10492891	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11150335	0.93[EUR][1000 genomes]
rs11150336	0.85[ASN][1000 genomes]
rs11864984	0.98[ASN][1000 genomes]
rs12918429	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16944339	0.83[EUR][1000 genomes]
rs16944345	0.85[EUR][1000 genomes]
rs16944347	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16954366	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2011142	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2167890	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2194323	0.98[ASN][1000 genomes]
rs2549822	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2549825	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2549831	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2549832	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2549834	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2549860	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2602450	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28659930	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28688510	0.95[ASN][1000 genomes]
rs2970080	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7201499	0.96[ASN][1000 genomes]
rs9921348	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9929815	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9931063	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9939934	0.91[AMR][1000 genomes];0.92[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	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1058045	chr16:80918138-81048242	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription 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	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81037800-81042400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr16:81038200-81042400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:81038400-81042200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr16:81038400-81042200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:81038800-81042200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr16:81038800-81042200	Active TSS	A549	lung
7	chr16:81038800-81042400	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr16:81039400-81042200	Active TSS	Colonic Mucosa	Colon
9	chr16:81039400-81042400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr16:81039400-81042400	Active TSS	NHLF	lung
11	chr16:81039600-81042200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr16:81039600-81042200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:81039600-81042200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:81039600-81042200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr16:81039600-81042200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:81039600-81042200	Active TSS	Fetal Intestine Large	intestine
17	chr16:81039600-81042200	Active TSS	Fetal Stomach	stomach
18	chr16:81039600-81042200	Active TSS	NHDF-Ad	bronchial
19	chr16:81039600-81042400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr16:81039600-81042400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:81039600-81042400	Active TSS	Brain Germinal Matrix	brain
22	chr16:81039600-81042400	Active TSS	Brain Hippocampus Middle	brain
23	chr16:81039600-81042400	Active TSS	HSMM	muscle
24	chr16:81039800-81042200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr16:81039800-81042200	Active TSS	Colon Smooth Muscle	Colon
26	chr16:81039800-81042200	Active TSS	Fetal Kidney	kidney
27	chr16:81039800-81042200	Active TSS	Rectal Smooth Muscle	rectum
28	chr16:81039800-81042200	Active TSS	Thymus	Thymus
29	chr16:81039800-81042200	Active TSS	NH-A	brain
30	chr16:81039800-81042400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr16:81039800-81042400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:81039800-81042600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:81040000-81042200	Active TSS	Primary T cells from cord blood	blood
34	chr16:81040000-81042200	Active TSS	Fetal Lung	lung
35	chr16:81040000-81042400	Active TSS	Fetal Muscle Trunk	muscle
36	chr16:81040800-81042200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:81041200-81042200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr16:81041200-81042400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr16:81041400-81042200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr16:81041400-81042200	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr16:81041400-81042200	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr16:81041400-81042200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr16:81041400-81042200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr16:81041400-81042200	Flanking Active TSS	Placenta	Placenta
45	chr16:81041600-81042200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr16:81041600-81042200	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr16:81041600-81042200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr16:81041600-81042200	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr16:81041600-81042200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr16:81041600-81042400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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