Variant report

Variant	rs12446424
Chromosome Location	chr16:80645662-80645663
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80631139..80633320-chr16:80645177..80647341,2	MCF-7	breast:
2	chr16:80644852..80647194-chr16:80651034..80653293,2	MCF-7	breast:
3	chr16:80567126..80568902-chr16:80645510..80647284,2	MCF-7	breast:
4	chr16:80644284..80647227-chr16:80651769..80654073,2	K562	blood:
5	chr16:80573033..80575436-chr16:80644795..80647684,3	MCF-7	breast:
6	chr16:80643464..80646861-chr16:80834784..80838958,5	MCF-7	breast:
7	chr16:80616339..80621061-chr16:80643147..80647399,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166446	Chromatin interaction
ENSG00000168589	Chromatin interaction
ENSG00000259867	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10468364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11866077	0.85[CEU][hapmap]
rs13329835	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs1629	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs17750740	0.93[CEU][hapmap]
rs2060861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2167671	0.94[EUR][1000 genomes]
rs2316184	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28456059	0.94[ASN][1000 genomes]
rs28650484	0.93[ASN][1000 genomes]
rs4613079	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4889165	1.00[JPT][hapmap]
rs6420415	0.93[CEU][hapmap]
rs6564770	0.92[CEU][hapmap]
rs6564771	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7187794	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs735753	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7404848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7499149	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7500067	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056731	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs873994	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs873995	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs879843	0.94[EUR][1000 genomes]
rs896625	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933302	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9938021	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940301	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9940376	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1056083	chr16:80636184-80666779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063971	chr16:80640278-80663092	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1063761	chr16:80640278-80663665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80626800-80645800	Weak transcription	Right Ventricle	heart
2	chr16:80629200-80647600	Weak transcription	NHEK	skin
3	chr16:80630600-80668000	Weak transcription	Fetal Kidney	kidney
4	chr16:80634000-80647800	Weak transcription	NHLF	lung
5	chr16:80634200-80663600	Weak transcription	Brain Anterior Caudate	brain
6	chr16:80635000-80651200	Weak transcription	Brain Hippocampus Middle	brain
7	chr16:80635400-80655600	Weak transcription	Brain Angular Gyrus	brain
8	chr16:80636000-80648200	Strong transcription	Hela-S3	cervix
9	chr16:80636400-80647800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr16:80636800-80653600	Weak transcription	HSMMtube	muscle
11	chr16:80637000-80653400	Weak transcription	HSMM	muscle
12	chr16:80637200-80648200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:80637400-80648600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr16:80637800-80647200	Strong transcription	Fetal Intestine Small	intestine
15	chr16:80638600-80645800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr16:80638600-80648000	Weak transcription	Left Ventricle	heart
17	chr16:80639800-80657400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr16:80640400-80647800	Weak transcription	Esophagus	oesophagus
19	chr16:80640600-80646200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr16:80640600-80652600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr16:80640600-80662200	Weak transcription	Primary T cells from cord blood	blood
22	chr16:80640600-80662600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr16:80640800-80663800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr16:80640800-80669200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr16:80641400-80646800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:80641400-80647000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:80641800-80652200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr16:80642000-80648200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr16:80642200-80652200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr16:80642200-80668200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:80642800-80663800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr16:80643000-80649600	Weak transcription	Fetal Stomach	stomach
33	chr16:80643000-80654600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:80643200-80648200	Weak transcription	HUVEC	blood vessel
35	chr16:80644200-80646000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:80644200-80647000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr16:80644200-80647200	Weak transcription	Fetal Lung	lung
38	chr16:80644200-80666200	Weak transcription	Brain Substantia Nigra	brain
39	chr16:80644600-80646600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr16:80644600-80646600	Strong transcription	Liver	Liver
41	chr16:80644600-80646600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr16:80644600-80646800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr16:80644600-80647000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr16:80644600-80647000	Strong transcription	Gastric	stomach
45	chr16:80644800-80646200	Genic enhancers	Placenta	Placenta
46	chr16:80644800-80646800	Strong transcription	Adipose Nuclei	Adipose
47	chr16:80645000-80646600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr16:80645000-80646800	Strong transcription	Spleen	Spleen
49	chr16:80645200-80646400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr16:80645200-80646600	Strong transcription	Primary monocytes fromperipheralblood	blood

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