Variant report

Variant	rs12341403
Chromosome Location	chr9:97159686-97159687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10115864	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10122398	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10125744	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10283669	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061835	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993191	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993194	0.85[ASN][1000 genomes]
rs12338572	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12343123	0.90[ASN][1000 genomes]
rs28567659	0.80[ASN][1000 genomes]
rs28704121	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28802403	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55936246	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55962682	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56165201	0.80[ASN][1000 genomes]
rs56404236	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479541	0.87[ASN][1000 genomes]
rs6479545	0.81[ASN][1000 genomes]
rs7024607	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7025878	0.83[ASN][1000 genomes]
rs7030326	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030967	0.90[ASN][1000 genomes]
rs7034153	0.81[ASN][1000 genomes]
rs7036474	0.85[ASN][1000 genomes]
rs7037298	0.81[ASN][1000 genomes]
rs7040774	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7041219	0.81[ASN][1000 genomes]
rs7045712	0.88[ASN][1000 genomes]
rs7046779	0.88[ASN][1000 genomes]
rs7856786	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859955	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9632920	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12341403	HIATL1	cis	Esophagus Mucosa	GTEx
rs12341403	HIATL1	cis	Adipose Subcutaneous	GTEx
rs12341403	HIATL1	cis	Skin Sun Exposed Lower leg	GTEx
rs12341403	HIATL1	cis	Thyroid	GTEx
rs12341403	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs12341403	HIATL1	cis	Esophagus Muscularis	GTEx
rs12341403	HIATL1	cis	lung	GTEx
rs12341403	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs12341403	HIATL1	cis	Nerve Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97138200-97162400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:97138800-97168600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97148800-97165400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:97150000-97166200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:97150200-97160000	Weak transcription	K562	blood
6	chr9:97151400-97175600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:97153000-97164000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:97153800-97182200	Weak transcription	NHEK	skin
9	chr9:97157000-97166400	Weak transcription	A549	lung
10	chr9:97157600-97165600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:97157800-97161200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr9:97158000-97203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:97158200-97160600	Weak transcription	Fetal Stomach	stomach
14	chr9:97159200-97160000	Weak transcription	Dnd41	blood
15	chr9:97159400-97160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:97159600-97160000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr9:97159600-97160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:97159600-97160200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:97159600-97160200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:97159600-97160200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr9:97159600-97160200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
22	chr9:97159600-97160200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:97159600-97160200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr9:97159600-97160200	Enhancers	GM12878-XiMat	blood
25	chr9:97159600-97160200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr9:97159600-97160400	Strong transcription	Primary B cells from peripheral blood	blood
27	chr9:97159600-97160800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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