Variant report

Variant	rs2549890
Chromosome Location	chr16:81079399-81079400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81071649..81074411-chr16:81077568..81081037,5	K562	blood:
2	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:
3	chr16:81079124..81081324-chr16:81108585..81111174,2	K562	blood:
4	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:
5	chr16:81078751..81080848-chr16:81181095..81182686,2	K562	blood:
6	chr16:81078691..81081572-chr16:81082090..81085180,4	K562	blood:
7	chr16:81074762..81077123-chr16:81078708..81080321,2	K562	blood:
8	chr16:81076434..81078165-chr16:81078716..81082306,3	MCF-7	breast:
9	chr16:81069446..81072291-chr16:81077678..81081761,3	K562	blood:
10	chr16:81075103..81077247-chr16:81078361..81079890,2	MCF-7	breast:
11	chr16:81068994..81072999-chr16:81079171..81083841,7	MCF-7	breast:
12	chr16:81072851..81076497-chr16:81077627..81082197,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1563076	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2549889	0.84[AFR][1000 genomes]
rs2549894	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2602432	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2602451	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2602454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2911157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889232	1.00[AMR][1000 genomes]
rs5023851	1.00[AMR][1000 genomes]
rs6420420	1.00[AMR][1000 genomes]
rs7187102	1.00[AMR][1000 genomes]
rs7196170	1.00[AMR][1000 genomes]
rs804888	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs804898	1.00[AMR][1000 genomes]
rs804901	1.00[AMR][1000 genomes]
rs8049509	0.81[AFR][1000 genomes]
rs8177931	1.00[AMR][1000 genomes]
rs935945	0.96[AFR][1000 genomes];1.00[AMR][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	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	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
4	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
5	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
6	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
7	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
8	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
9	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr16:81071200-81080400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:81071200-81080400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr16:81071200-81080600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr16:81071200-81082000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:81071200-81082400	Weak transcription	Stomach Mucosa	stomach
8	chr16:81071400-81079400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr16:81071400-81079600	Strong transcription	Fetal Muscle Trunk	muscle
10	chr16:81071400-81079800	Strong transcription	Fetal Intestine Large	intestine
11	chr16:81071600-81080600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:81071800-81081800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr16:81072000-81079400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:81072200-81079400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr16:81072400-81079800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr16:81073000-81079800	Strong transcription	Fetal Muscle Leg	muscle
17	chr16:81073600-81079800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr16:81073800-81079400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr16:81073800-81079800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr16:81073800-81079800	Strong transcription	Fetal Thymus	thymus
21	chr16:81073800-81079800	Strong transcription	Dnd41	blood
22	chr16:81074000-81079400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:81074000-81079400	Strong transcription	Lung	lung
24	chr16:81074000-81079400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr16:81074000-81079800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr16:81074000-81079800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr16:81074000-81080000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr16:81074000-81080400	Strong transcription	Primary B cells from cord blood	blood
29	chr16:81074000-81080400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr16:81074000-81082400	Weak transcription	Fetal Heart	heart
31	chr16:81074200-81079400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:81074200-81079800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:81074400-81079400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr16:81074400-81079400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:81074400-81079400	Strong transcription	HMEC	breast
36	chr16:81074400-81079400	Strong transcription	HUVEC	blood vessel
37	chr16:81074400-81079800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:81074400-81079800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr16:81074400-81079800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr16:81074400-81079800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr16:81074400-81079800	Strong transcription	Liver	Liver
42	chr16:81074400-81079800	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr16:81074400-81080000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr16:81074400-81080200	Strong transcription	Primary T cells from cord blood	blood
45	chr16:81074600-81079400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr16:81074600-81079400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr16:81074600-81079600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:81074600-81079600	Strong transcription	HSMM	muscle
49	chr16:81074600-81079800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr16:81074600-81080000	Strong transcription	A549	lung

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