Variant report

Variant	rs56117588
Chromosome Location	chr16:77231042-77231043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:77223534..77226455-chr16:77227601..77231752,9	MCF-7	breast:
2	chr16:77226552..77228605-chr16:77230718..77233124,2	MCF-7	breast:
3	chr16:77228552..77231268-chr16:77235268..77236824,2	MCF-7	breast:
4	chr16:77223627..77226316-chr16:77230976..77234622,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103111	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1025319	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12051195	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12051196	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12051533	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12149296	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17769233	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2052876	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2052877	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2232497	0.90[ASN][1000 genomes]
rs2232498	0.92[ASN][1000 genomes]
rs2232506	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278044	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2303259	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55638906	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55717232	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55892569	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55993423	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56321825	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57007576	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59374564	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66611567	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66665417	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66773611	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66781272	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67076559	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67133421	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67921380	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68005990	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68097506	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs68164273	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68184079	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7184316	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7199027	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72628222	0.80[EUR][1000 genomes]
rs72798552	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746036	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs755255	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8045096	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051242	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8182187	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][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	nsv869201	chr16:76714549-77233646	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77226200-77233000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:77226200-77240400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr16:77226400-77240200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr16:77226600-77233800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:77226600-77233800	Strong transcription	A549	lung
6	chr16:77226600-77234200	Strong transcription	Fetal Muscle Leg	muscle
7	chr16:77226600-77235000	Weak transcription	Psoas Muscle	Psoas
8	chr16:77226600-77235600	Strong transcription	Fetal Thymus	thymus
9	chr16:77226800-77233400	Strong transcription	NHLF	lung
10	chr16:77226800-77233800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr16:77226800-77233800	Strong transcription	Colonic Mucosa	Colon
12	chr16:77226800-77233800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr16:77226800-77234000	Strong transcription	Thymus	Thymus
14	chr16:77226800-77234000	Strong transcription	K562	blood
15	chr16:77226800-77234600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr16:77226800-77235200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr16:77226800-77235600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:77226800-77235600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:77226800-77235600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr16:77227000-77231200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr16:77227000-77232400	Weak transcription	Stomach Mucosa	stomach
22	chr16:77227000-77233800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr16:77227000-77233800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr16:77227000-77234000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:77227000-77234000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr16:77227000-77235600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr16:77227000-77235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr16:77227000-77235600	Strong transcription	Liver	Liver
29	chr16:77227000-77235800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr16:77227000-77236200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr16:77227000-77236600	Strong transcription	Primary T cells from cord blood	blood
32	chr16:77227000-77246000	Weak transcription	Fetal Heart	heart
33	chr16:77227200-77233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:77227200-77233400	Strong transcription	Brain Substantia Nigra	brain
35	chr16:77227200-77233800	Strong transcription	Rectal Smooth Muscle	rectum
36	chr16:77227200-77234000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr16:77227200-77234000	Strong transcription	Fetal Intestine Small	intestine
38	chr16:77227200-77234000	Strong transcription	Left Ventricle	heart
39	chr16:77227200-77234200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr16:77227200-77234600	Strong transcription	Fetal Stomach	stomach
41	chr16:77227200-77235600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:77227200-77235600	Strong transcription	Placenta	Placenta
43	chr16:77227200-77245800	Weak transcription	Fetal Kidney	kidney
44	chr16:77227200-77247200	Weak transcription	Hela-S3	cervix
45	chr16:77227400-77233000	Weak transcription	Small Intestine	intestine
46	chr16:77227400-77233400	Strong transcription	Aorta	Aorta
47	chr16:77227400-77233800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr16:77227400-77233800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr16:77227400-77234000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr16:77227400-77234000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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