Variant report

Variant	rs12338230
Chromosome Location	chr9:97226466-97226467
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97220678..97222830-chr9:97224349..97226700,3	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10114295	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10116979	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10122398	0.81[ASN][1000 genomes]
rs10125631	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10125744	0.81[ASN][1000 genomes]
rs10441776	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10993194	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338572	0.81[ASN][1000 genomes]
rs12343123	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12343977	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16911832	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2406663	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28459299	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28477240	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28575335	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28715696	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28802403	0.81[ASN][1000 genomes]
rs55936246	0.81[ASN][1000 genomes]
rs55962682	0.81[ASN][1000 genomes]
rs56413623	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6479541	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6479545	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6479549	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7022386	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7025878	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7027704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027860	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7028388	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7030967	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7034153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7036474	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7037298	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7041219	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7042219	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7042434	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7042468	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7045712	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7046779	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73529936	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7850084	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7858126	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7868600	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7868703	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7873527	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs908808	0.86[EUR][1000 genomes]
rs9632920	0.81[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	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	nsv893593	chr9:97196979-97228918	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	esv1840205	chr9:97202200-97366400	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv893594	chr9:97221463-97283226	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12338230	HIATL1	cis	Nerve Tibial	GTEx
rs12338230	HIATL1	cis	Adipose Subcutaneous	GTEx
rs12338230	HIATL1	cis	lung	GTEx
rs12338230	HIATL1	cis	Esophagus Mucosa	GTEx
rs12338230	HIATL1	Cis_1M	lymphoblastoid	RTeQTL
rs12338230	HIATL1	cis	Thyroid	GTEx
rs12338230	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs12338230	HIATL1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97204400-97227000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:97217000-97226600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:97220400-97227000	Weak transcription	Gastric	stomach
4	chr9:97222200-97227000	Weak transcription	Esophagus	oesophagus
5	chr9:97222600-97237800	Weak transcription	Stomach Mucosa	stomach
6	chr9:97222800-97226600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97222800-97226800	Weak transcription	Left Ventricle	heart
8	chr9:97223600-97226600	Weak transcription	Fetal Thymus	thymus
9	chr9:97223800-97226800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr9:97224000-97226600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr9:97224200-97226800	Weak transcription	Fetal Brain Male	brain
12	chr9:97224200-97227000	Weak transcription	Liver	Liver
13	chr9:97224200-97227000	Weak transcription	Psoas Muscle	Psoas
14	chr9:97224400-97226600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr9:97224400-97226600	Weak transcription	Brain Substantia Nigra	brain
16	chr9:97224400-97226600	Weak transcription	Fetal Brain Female	brain
17	chr9:97224400-97226600	Weak transcription	Osteobl	bone
18	chr9:97224400-97227800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr9:97224600-97226600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:97224600-97226800	Weak transcription	NH-A	brain
21	chr9:97224600-97227000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:97225000-97226600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:97225000-97226600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:97225000-97226800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr9:97225000-97227200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:97225200-97226600	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:97225200-97226600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:97225200-97226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:97225200-97226800	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:97225200-97226800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:97225200-97226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr9:97225200-97227000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:97225200-97227000	Weak transcription	Aorta	Aorta
34	chr9:97225200-97227000	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr9:97225200-97227000	Weak transcription	Placenta	Placenta
36	chr9:97225200-97227400	Weak transcription	HUVEC	blood vessel
37	chr9:97225200-97228000	Weak transcription	HMEC	breast
38	chr9:97225400-97226600	Weak transcription	Primary T cells from cord blood	blood
39	chr9:97225400-97226600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:97225400-97226600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:97225400-97226600	Weak transcription	Brain Germinal Matrix	brain
42	chr9:97225400-97227000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97225400-97227200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:97225400-97227200	Weak transcription	Thymus	Thymus
45	chr9:97225400-97228000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:97225400-97228200	Weak transcription	NHEK	skin
47	chr9:97225600-97226600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr9:97225600-97226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr9:97225600-97226600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr9:97225600-97226800	Weak transcription	Ovary	ovary

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