Variant report

Variant	rs12596549
Chromosome Location	chr16:12183500-12183501
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12174212..12176270-chr16:12182353..12184871,2	K562	blood:

Variant related genes	Relation type
ENSG00000241641	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11075049	0.81[ASN][1000 genomes]
rs11075054	0.81[ASN][1000 genomes]
rs11639701	0.94[ASN][1000 genomes]
rs11642033	0.85[ASN][1000 genomes]
rs11642386	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11646458	0.88[ASN][1000 genomes]
rs11646539	0.81[ASN][1000 genomes]
rs11646584	0.85[ASN][1000 genomes]
rs11647572	0.82[ASN][1000 genomes]
rs11648228	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648468	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11648816	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12596703	0.82[ASN][1000 genomes]
rs12599090	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12599793	0.81[ASN][1000 genomes]
rs12708746	0.80[ASN][1000 genomes]
rs12926900	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12929519	0.85[ASN][1000 genomes]
rs13336687	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958964	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457193	0.86[ASN][1000 genomes]
rs28439695	0.87[ASN][1000 genomes]
rs28667047	0.86[ASN][1000 genomes]
rs2869808	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs350264	0.86[ASN][1000 genomes]
rs350265	0.82[ASN][1000 genomes]
rs350266	0.82[ASN][1000 genomes]
rs35053871	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35318501	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35542345	0.85[ASN][1000 genomes]
rs3851011	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851012	0.95[ASN][1000 genomes]
rs4780411	0.98[ASN][1000 genomes]
rs4781180	0.99[ASN][1000 genomes]
rs71385189	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7200307	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8048589	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050180	0.88[ASN][1000 genomes]
rs8055516	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8059989	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8062015	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8063329	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925009	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9935284	0.81[ASN][1000 genomes]
rs9936270	0.80[ASN][1000 genomes]
rs9939383	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1039492	chr16:12176517-12210702	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12142800-12189200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr16:12156000-12185800	Weak transcription	Brain Germinal Matrix	brain
3	chr16:12156000-12185800	Weak transcription	Fetal Brain Female	brain
4	chr16:12157200-12185800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:12157800-12185800	Weak transcription	HSMMtube	muscle
6	chr16:12163600-12183600	Weak transcription	Colon Smooth Muscle	Colon
7	chr16:12167600-12185800	Weak transcription	HSMM	muscle
8	chr16:12175200-12185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr16:12178600-12199600	Weak transcription	Aorta	Aorta
10	chr16:12181400-12183600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr16:12181400-12183600	Enhancers	Stomach Mucosa	stomach
12	chr16:12181600-12184200	Enhancers	Placenta	Placenta
13	chr16:12181600-12184400	Enhancers	Primary B cells from cord blood	blood
14	chr16:12181600-12184400	Enhancers	Esophagus	oesophagus
15	chr16:12181800-12184400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr16:12181800-12184400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr16:12182000-12183600	Weak transcription	Brain Substantia Nigra	brain
18	chr16:12182200-12183600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr16:12182200-12188600	Weak transcription	Fetal Brain Male	brain
20	chr16:12182800-12184200	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr16:12182800-12184200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr16:12182800-12184400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr16:12183000-12183600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr16:12183000-12183600	Enhancers	Fetal Muscle Leg	muscle
25	chr16:12183200-12183600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr16:12183200-12183600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr16:12183200-12183600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr16:12183200-12183600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:12183200-12183600	Enhancers	Brain Cingulate Gyrus	brain
30	chr16:12183200-12183600	Enhancers	Brain Hippocampus Middle	brain
31	chr16:12183200-12183600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr16:12183200-12183600	Enhancers	Fetal Kidney	kidney
33	chr16:12183200-12183600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr16:12183200-12183600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr16:12183200-12183800	Enhancers	NHLF	lung
36	chr16:12183200-12184000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:12183200-12184000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr16:12183200-12184000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr16:12183200-12184000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr16:12183200-12184000	Enhancers	Liver	Liver
41	chr16:12183200-12184000	Flanking Active TSS	NH-A	brain
42	chr16:12183200-12184200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr16:12183200-12184200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:12183200-12184200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr16:12183200-12184200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr16:12183200-12184200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr16:12183200-12184200	Flanking Active TSS	Thymus	Thymus
48	chr16:12183200-12184400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr16:12183200-12184400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr16:12183200-12184600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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