Variant report

Variant	rs12596662
Chromosome Location	chr16:75693029-75693030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75654334..75656707-chr16:75691498..75693469,2	K562	blood:
2	chr16:75691958..75693608-chr16:75693696..75696714,3	MCF-7	breast:
3	chr16:75681364..75684772-chr16:75690611..75693134,4	K562	blood:

Variant related genes	Relation type
ENSG00000065427	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000166848	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10781978	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11149843	0.88[ASN][1000 genomes]
rs1874022	0.92[ASN][1000 genomes]
rs4888441	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4888443	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs55864135	0.92[ASN][1000 genomes]
rs59297469	0.81[AFR][1000 genomes]
rs61310184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050949	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8057353	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS 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	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS 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	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12596662	ADAT1	cis	Esophagus Mucosa	GTEx
rs12596662	ADAT1	cis	Thyroid	GTEx
rs12596662	ADAT1	cis	Adipose Subcutaneous	GTEx
rs12596662	ADAT1	cis	Esophagus Muscularis	GTEx
rs12596662	ADAT1	cis	Artery Tibial	GTEx
rs12596662	ADAT1	cis	Muscle Skeletal	GTEx
rs12596662	ADAT1	cis	Nerve Tibial	GTEx
rs12596662	ADAT1	Cis_1M	lymphoblastoid	RTeQTL
rs12596662	ADAT1	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75684600-75695400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:75686200-75694400	Weak transcription	Right Atrium	heart
3	chr16:75686400-75695800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:75686600-75695200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr16:75687000-75695400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr16:75687400-75693600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:75687400-75696000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr16:75687600-75693600	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr16:75687600-75694200	Strong transcription	Fetal Muscle Leg	muscle
10	chr16:75687600-75694600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr16:75687600-75695600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:75687600-75696000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:75687600-75696000	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr16:75687600-75696400	Strong transcription	Primary B cells from cord blood	blood
15	chr16:75687600-75696400	Strong transcription	Fetal Stomach	stomach
16	chr16:75687800-75693400	Strong transcription	Left Ventricle	heart
17	chr16:75687800-75694200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr16:75687800-75694600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr16:75687800-75694800	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr16:75687800-75695400	Strong transcription	Fetal Thymus	thymus
21	chr16:75687800-75695800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr16:75687800-75696200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr16:75687800-75696200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr16:75688000-75693400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr16:75688000-75693800	Strong transcription	Fetal Intestine Large	intestine
26	chr16:75688000-75694000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:75688000-75694200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr16:75688000-75694800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr16:75688000-75695200	Strong transcription	Liver	Liver
30	chr16:75688000-75695200	Strong transcription	GM12878-XiMat	blood
31	chr16:75688000-75695800	Strong transcription	Placenta	Placenta
32	chr16:75688200-75693600	Strong transcription	NH-A	brain
33	chr16:75688200-75693800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:75688200-75693800	Strong transcription	Brain Germinal Matrix	brain
35	chr16:75688200-75695800	Strong transcription	Primary T cells from cord blood	blood
36	chr16:75688200-75696000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr16:75688200-75696000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:75688400-75693600	Strong transcription	Dnd41	blood
39	chr16:75688400-75693800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr16:75688400-75693800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr16:75688400-75694200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr16:75688400-75695600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr16:75688400-75695600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr16:75688400-75695800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:75688400-75696000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr16:75688400-75696000	Strong transcription	NHDF-Ad	bronchial
47	chr16:75688600-75693600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:75688600-75693600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr16:75688600-75694600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr16:75688600-75695600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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