Variant report

Variant	rs17109188
Chromosome Location	chr14:39868032-39868033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs17109174	0.87[YRI][hapmap];1.00[AFR][1000 genomes]
rs17109213	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109227	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109249	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17109331	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34909359	1.00[AMR][1000 genomes]
rs56859252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57012657	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57430547	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57569191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57600452	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58889517	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59546917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59597680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59741982	1.00[AMR][1000 genomes]
rs59953702	1.00[AMR][1000 genomes]
rs60367463	1.00[AMR][1000 genomes]
rs60601774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60921042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61176483	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61549948	1.00[AMR][1000 genomes]
rs61668966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7148519	1.00[AMR][1000 genomes]
rs73275040	1.00[AMR][1000 genomes]
rs73275059	1.00[AMR][1000 genomes]
rs73275062	1.00[AMR][1000 genomes]
rs73275075	1.00[AMR][1000 genomes]
rs73275076	1.00[AMR][1000 genomes]
rs73277428	1.00[AMR][1000 genomes]
rs73277432	1.00[AMR][1000 genomes]
rs73277440	1.00[AMR][1000 genomes]
rs73277451	1.00[AMR][1000 genomes]
rs73277466	1.00[AMR][1000 genomes]
rs73277467	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277471	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277473	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277474	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277475	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277478	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277496	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277499	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73277501	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279309	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73279392	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283432	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283442	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73285599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73287602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73291685	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293637	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17109188	FOXG1	trans	lymphoblastoid	seeQTL
rs17109188	FBXO33	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
2	chr14:39835400-39872400	Weak transcription	Fetal Muscle Leg	muscle
3	chr14:39836200-39872800	Weak transcription	Esophagus	oesophagus
4	chr14:39836400-39870600	Weak transcription	Gastric	stomach
5	chr14:39840000-39882600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:39846200-39878800	Weak transcription	Right Ventricle	heart
7	chr14:39846800-39872400	Weak transcription	HSMMtube	muscle
8	chr14:39850400-39870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:39851200-39868600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr14:39851400-39868600	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:39851400-39868600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr14:39853600-39874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr14:39854400-39872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:39855400-39868800	Weak transcription	Aorta	Aorta
15	chr14:39857000-39870400	Weak transcription	Brain Germinal Matrix	brain
16	chr14:39860200-39882200	Weak transcription	Fetal Heart	heart
17	chr14:39860400-39868600	Weak transcription	A549	lung
18	chr14:39860800-39868400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr14:39861000-39868400	Weak transcription	Hela-S3	cervix
20	chr14:39861200-39871800	Weak transcription	Fetal Brain Male	brain
21	chr14:39861200-39872200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr14:39861400-39874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:39861800-39872000	Weak transcription	K562	blood
24	chr14:39862000-39868800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:39862000-39886000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr14:39862400-39870800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:39862400-39871000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr14:39862400-39871200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr14:39862400-39871400	Strong transcription	Liver	Liver
30	chr14:39862400-39874800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr14:39862600-39868400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr14:39862600-39868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:39862600-39871000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr14:39862600-39871200	Strong transcription	Adipose Nuclei	Adipose
35	chr14:39862800-39871200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr14:39862800-39871200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr14:39863200-39868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr14:39863200-39870800	Weak transcription	Brain Substantia Nigra	brain
39	chr14:39863200-39873000	Weak transcription	Lung	lung
40	chr14:39863400-39870400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr14:39863400-39871200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr14:39863400-39872000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr14:39863400-39874000	Weak transcription	Fetal Lung	lung
44	chr14:39863400-39891600	Weak transcription	Small Intestine	intestine
45	chr14:39863600-39871200	Strong transcription	Primary T cells from cord blood	blood
46	chr14:39863800-39872600	Weak transcription	Spleen	Spleen
47	chr14:39864000-39870400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr14:39864000-39871000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr14:39864600-39868800	Weak transcription	Colon Smooth Muscle	Colon
50	chr14:39864600-39869200	Strong transcription	Fetal Intestine Large	intestine

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