Variant report

Variant	rs4889534
Chromosome Location	chr16:30865440-30865441
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30864015..30867416-chr16:30933268..30936287,3	MCF-7	breast:
2	chr16:30864812..30866480-chr16:30884926..30886769,2	MCF-7	breast:
3	chr16:30863260..30865823-chr16:30870781..30872827,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099364	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000260083	Chromatin interaction
ENSG00000260852	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11150596	0.84[ASN][1000 genomes]
rs11150599	0.84[ASN][1000 genomes]
rs11647697	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862962	0.86[ASN][1000 genomes]
rs11864054	0.84[ASN][1000 genomes]
rs12920259	0.89[ASN][1000 genomes]
rs12926295	0.89[ASN][1000 genomes]
rs12928081	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12929065	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12930944	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12931096	0.80[AFR][1000 genomes]
rs1458201	0.84[CEU][hapmap]
rs2125293	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168834	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335013	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878304	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34840035	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35675346	0.84[CEU][hapmap]
rs4290486	0.89[ASN][1000 genomes]
rs4889536	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889614	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4889622	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889627	0.97[ASN][1000 genomes]
rs4889630	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4889631	0.96[AFR][1000 genomes]
rs4889651	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4889653	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55719146	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56083427	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67264578	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67456613	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7200879	0.84[CEU][hapmap]
rs72799330	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7500719	0.84[ASN][1000 genomes]
rs8046391	0.80[CEU][hapmap]
rs8050107	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8059475	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8063565	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs897984	0.89[ASN][1000 genomes]
rs9796842	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9932572	0.84[ASN][1000 genomes]
rs9933843	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
5	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
6	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
7	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
8	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
9	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv1060384	chr16:30802415-30878838	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1059633	chr16:30803099-30867916	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases
13	nsv833190	chr16:30845051-31007863	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
14	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30845800-30884800	Weak transcription	Brain Germinal Matrix	brain
2	chr16:30846400-30883400	Weak transcription	Fetal Brain Female	brain
3	chr16:30846800-30885600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr16:30856200-30885800	Weak transcription	NH-A	brain
5	chr16:30856400-30883400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr16:30856600-30867800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr16:30856600-30869200	Weak transcription	HSMM	muscle
8	chr16:30856600-30883400	Weak transcription	Lung	lung
9	chr16:30856600-30885000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr16:30856800-30869600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr16:30856800-30871200	Weak transcription	Aorta	Aorta
12	chr16:30856800-30882400	Weak transcription	Brain Substantia Nigra	brain
13	chr16:30856800-30883400	Weak transcription	Pancreas	Pancrea
14	chr16:30856800-30883600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:30856800-30883600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr16:30856800-30883600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:30856800-30885600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr16:30856800-30885600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:30856800-30885600	Weak transcription	Esophagus	oesophagus
20	chr16:30856800-30885600	Weak transcription	Spleen	Spleen
21	chr16:30856800-30885800	Weak transcription	Brain Angular Gyrus	brain
22	chr16:30857000-30866000	Weak transcription	Fetal Intestine Small	intestine
23	chr16:30857000-30867800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr16:30857000-30868000	Weak transcription	HepG2	liver
25	chr16:30857000-30868200	Weak transcription	Primary T cells from cord blood	blood
26	chr16:30857000-30868200	Weak transcription	Right Ventricle	heart
27	chr16:30857000-30869600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr16:30857000-30883200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:30857000-30883400	Weak transcription	Ovary	ovary
30	chr16:30857000-30883800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr16:30857000-30885400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr16:30857000-30885600	Weak transcription	Brain Hippocampus Middle	brain
33	chr16:30858400-30866600	Weak transcription	Left Ventricle	heart
34	chr16:30858800-30869400	Weak transcription	Psoas Muscle	Psoas
35	chr16:30858800-30869800	Weak transcription	HSMMtube	muscle
36	chr16:30858800-30885800	Weak transcription	NHDF-Ad	bronchial
37	chr16:30862000-30867200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr16:30862800-30866600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr16:30863000-30866400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:30863600-30866600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr16:30863600-30885600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr16:30864200-30866800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:30864400-30865800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr16:30864400-30866600	Enhancers	NHEK	skin
45	chr16:30864400-30869800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr16:30864600-30865800	Strong transcription	Primary B cells from cord blood	blood
47	chr16:30864600-30866000	Strong transcription	Fetal Lung	lung
48	chr16:30864600-30866000	Strong transcription	Fetal Muscle Leg	muscle
49	chr16:30864600-30866000	Enhancers	HMEC	breast
50	chr16:30864600-30866400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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