Variant report

Variant	rs13299029
Chromosome Location	chr9:99983093-99983094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10116019	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10119245	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759522	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817265	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10981209	0.80[EUR][1000 genomes]
rs12235734	0.82[EUR][1000 genomes]
rs28846196	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3957904	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3994556	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4626726	0.80[EUR][1000 genomes]
rs6478015	0.82[AMR][1000 genomes]
rs6478020	0.81[AMR][1000 genomes]
rs7022475	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7850392	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7850429	0.85[AMR][1000 genomes]
rs7850504	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7855366	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7855622	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7868440	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7868563	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7868806	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7869509	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7869568	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7869587	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7869959	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv972433	chr9:99962059-99983443	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13299029	ANKRD18CP	cis	Thyroid	GTEx
rs13299029	RP11-520B13.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99976600-99985000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr9:99976600-99985000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:99976800-99985200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:99976800-99985400	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:99981400-99985000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr9:99981800-99985000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:99982000-99985000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:99982000-99985200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:99982200-99983200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr9:99982200-99985200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr9:99982400-99983400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:99982400-99985200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:99983000-99983200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:99983000-99983200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr9:99983000-99983200	Active TSS	Brain Angular Gyrus	brain
16	chr9:99983000-99983200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
17	chr9:99983000-99983200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr9:99983000-99983200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr9:99983000-99983200	Bivalent Enhancer	Fetal Kidney	kidney
20	chr9:99983000-99983200	Enhancers	Right Ventricle	heart
21	chr9:99983000-99983400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr9:99983000-99983400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr9:99983000-99983400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:99983000-99983400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:99983000-99983400	Bivalent Enhancer	Colon Smooth Muscle	Colon
26	chr9:99983000-99984000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:99983000-99984400	Bivalent/Poised TSS	NHEK	skin
28	chr9:99983000-99984800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr9:99983000-99985000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:99983000-99985000	Active TSS	Brain Anterior Caudate	brain
31	chr9:99983000-99985200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr9:99983000-99985200	Bivalent Enhancer	Fetal Brain Male	brain

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