Variant report

Variant	rs12338572
Chromosome Location	chr9:97177641-97177642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10115864	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122398	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125744	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10283669	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1061835	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993191	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10993194	0.90[ASN][1000 genomes]
rs10993201	0.81[ASN][1000 genomes]
rs12338230	0.81[ASN][1000 genomes]
rs12341403	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12343123	0.95[ASN][1000 genomes]
rs16911832	0.80[ASN][1000 genomes]
rs1878875	0.85[ASN][1000 genomes]
rs28704121	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28802403	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55936246	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55962682	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56404236	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6479541	0.92[ASN][1000 genomes]
rs6479545	0.85[ASN][1000 genomes]
rs7024607	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7025878	0.88[ASN][1000 genomes]
rs7027704	0.81[ASN][1000 genomes]
rs7030326	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7030967	0.95[ASN][1000 genomes]
rs7034153	0.85[ASN][1000 genomes]
rs7036474	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7037298	0.85[ASN][1000 genomes]
rs7040774	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7041219	0.85[ASN][1000 genomes]
rs7045712	0.93[ASN][1000 genomes]
rs7046779	0.93[ASN][1000 genomes]
rs7856786	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7859955	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9632920	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv982324	chr9:97139062-97200156	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12338572	HIATL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12338572	HIATL1	cis	Thyroid	GTEx
rs12338572	HIATL1	cis	lung	GTEx
rs12338572	HIATL1	cis	Adipose Subcutaneous	GTEx
rs12338572	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs12338572	HIATL1	cis	Esophagus Mucosa	GTEx
rs12338572	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs12338572	HIATL1	cis	Nerve Tibial	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97153800-97182200	Weak transcription	NHEK	skin
2	chr9:97158000-97203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:97160200-97182400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:97160200-97183400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr9:97160400-97203600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr9:97164400-97185200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:97166400-97206400	Weak transcription	HSMMtube	muscle
8	chr9:97167800-97203600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:97169800-97207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:97171800-97178800	Weak transcription	Fetal Intestine Small	intestine
11	chr9:97172000-97186000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:97172000-97203200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr9:97172600-97204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:97172800-97182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:97173200-97184000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:97174200-97207000	Weak transcription	Lung	lung
18	chr9:97174400-97183800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:97175200-97178000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:97175600-97204200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:97175800-97202200	Weak transcription	Dnd41	blood
22	chr9:97176000-97183600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:97176000-97203800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:97176200-97178200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:97176200-97180200	Weak transcription	HSMM	muscle
26	chr9:97176200-97182200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:97176200-97182200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:97176200-97184600	Weak transcription	Primary T cells from cord blood	blood
29	chr9:97176200-97192200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:97176200-97194800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr9:97176200-97195000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:97176200-97201000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr9:97176200-97203200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:97176200-97203600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:97176200-97203600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
37	chr9:97176400-97183600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr9:97176400-97203200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:97176600-97179200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:97176600-97183600	Weak transcription	Adipose Nuclei	Adipose
41	chr9:97176600-97203400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr9:97176800-97178800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:97176800-97203200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:97176800-97203600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:97176800-97218000	Weak transcription	Fetal Brain Female	brain
46	chr9:97177000-97181400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:97177000-97203200	Weak transcription	Osteobl	bone
48	chr9:97177200-97201000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:97177200-97201000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr9:97177200-97203600	Weak transcription	Thymus	Thymus

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