Variant report

Variant	rs55892569
Chromosome Location	chr16:77244419-77244420
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	POLR2A	chr16:77244366-77244549	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr16:77244385-77244560	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr16:77243647-77245353	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:77223459..77226590-chr16:77240942..77244568,3	K562	blood:
2	chr16:77223687..77225503-chr16:77242852..77244719,2	MCF-7	breast:
3	chr16:77225300..77227094-chr16:77244120..77246217,2	MCF-7	breast:

Variant related genes	Relation type
SYCE1L	TF binding region
ENSG00000103111	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1025319	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12051195	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12051196	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12051533	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12149296	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17769233	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2052876	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2052877	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2078107	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2232497	0.92[ASN][1000 genomes]
rs2232498	0.94[ASN][1000 genomes]
rs2232506	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278044	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2303259	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55638906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55711425	0.82[EUR][1000 genomes]
rs55717232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55993423	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56117588	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56321825	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57007576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58938039	0.93[AMR][1000 genomes]
rs59374564	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66471623	0.82[EUR][1000 genomes]
rs66611567	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66665417	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66773611	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66781272	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66941815	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67076559	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67133421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67285321	0.81[EUR][1000 genomes]
rs67549301	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67910200	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67921380	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67992364	0.81[EUR][1000 genomes]
rs68005990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68083542	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68097506	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68164273	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68184079	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7184316	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7187474	0.82[ASN][1000 genomes]
rs7199027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72628222	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72798552	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs746036	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755255	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8045096	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8051242	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8182187	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929891	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065343	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv542965	chr16:76927295-77279747	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77227000-77246000	Weak transcription	Fetal Heart	heart
2	chr16:77227200-77245800	Weak transcription	Fetal Kidney	kidney
3	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
4	chr16:77233200-77245600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr16:77233200-77245600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:77233200-77245800	Weak transcription	NHEK	skin
7	chr16:77233400-77245000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:77233400-77245400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr16:77233400-77245600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr16:77233400-77245600	Weak transcription	HMEC	breast
11	chr16:77233400-77245600	Weak transcription	NH-A	brain
12	chr16:77233400-77246000	Weak transcription	Aorta	Aorta
13	chr16:77233400-77246000	Weak transcription	Brain Angular Gyrus	brain
14	chr16:77233400-77246000	Weak transcription	Brain Substantia Nigra	brain
15	chr16:77233800-77245400	Weak transcription	A549	lung
16	chr16:77233800-77245600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr16:77233800-77245600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr16:77233800-77245600	Weak transcription	Brain Germinal Matrix	brain
19	chr16:77233800-77245600	Weak transcription	Fetal Lung	lung
20	chr16:77233800-77245600	Weak transcription	HUVEC	blood vessel
21	chr16:77233800-77245800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr16:77233800-77245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr16:77233800-77245800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr16:77233800-77245800	Weak transcription	Fetal Brain Female	brain
25	chr16:77233800-77245800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr16:77233800-77246000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr16:77233800-77246000	Weak transcription	HSMMtube	muscle
28	chr16:77234000-77245400	Weak transcription	Pancreas	Pancrea
29	chr16:77234000-77245600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:77234000-77245600	Weak transcription	Esophagus	oesophagus
31	chr16:77234000-77245600	Weak transcription	Thymus	Thymus
32	chr16:77234000-77245800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr16:77234000-77245800	Weak transcription	Brain Anterior Caudate	brain
34	chr16:77234200-77245400	Weak transcription	Spleen	Spleen
35	chr16:77234200-77246000	Weak transcription	Lung	lung
36	chr16:77235200-77245800	Weak transcription	GM12878-XiMat	blood
37	chr16:77235200-77245800	Weak transcription	HSMM	muscle
38	chr16:77235200-77246000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr16:77235400-77245200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr16:77235600-77245400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:77235600-77245400	Weak transcription	Brain Hippocampus Middle	brain
42	chr16:77235600-77245600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr16:77235600-77245600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr16:77235600-77245600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr16:77235600-77245600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr16:77235600-77245600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr16:77235600-77245600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr16:77235600-77245600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr16:77235600-77245600	Weak transcription	Placenta	Placenta
50	chr16:77235600-77245600	Weak transcription	Fetal Thymus	thymus

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