Variant report

Variant	rs10739210
Chromosome Location	chr9:108463108-108463109
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr9:108462880-108463243	Hela-S3	cervix:	n/a	chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463057-108463070 chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463056-108463073 chr9:108463058-108463069
2	CEBPB	chr9:108462915-108463191	HepG2	liver:	n/a	chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463057-108463070 chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463056-108463073 chr9:108463058-108463069
3	MAX	chr9:108463048-108463397	NB4	blood:	n/a	chr9:108463234-108463244 chr9:108463222-108463232
4	CEBPB	chr9:108462862-108463255	K562	blood:	n/a	chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463057-108463070 chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463056-108463073 chr9:108463058-108463069
5	MAX	chr9:108462992-108463393	K562	blood:	n/a	chr9:108463234-108463244 chr9:108463222-108463232
6	CEBPB	chr9:108462919-108463180	ECC-1	luminal epithelium:	n/a	chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463057-108463070 chr9:108463057-108463068 chr9:108463057-108463070 chr9:108463056-108463073 chr9:108463058-108463069

Variant related genes	Relation type
TMEM38B	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10115634	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118720	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119254	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512339	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10733555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739209	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10739212	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759127	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10816293	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10978213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10978216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271247	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2271248	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3105993	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3126471	0.87[JPT][hapmap]
rs3793640	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477461	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7019359	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7026251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7039618	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039893	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7862873	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9299110	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893693	chr9:108427062-108683134	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10739210	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL
rs10739210	TMEM38B	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108457800-108463200	Weak transcription	Small Intestine	intestine
2	chr9:108457800-108472800	Weak transcription	Spleen	Spleen
3	chr9:108457800-108476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:108457800-108492200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:108458000-108468400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:108458000-108472400	Weak transcription	HSMM	muscle
7	chr9:108458000-108473000	Weak transcription	Left Ventricle	heart
8	chr9:108458000-108475200	Weak transcription	Fetal Thymus	thymus
9	chr9:108458000-108475600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr9:108458000-108475600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:108458000-108475600	Weak transcription	Thymus	Thymus
12	chr9:108458000-108476000	Weak transcription	Ovary	ovary
13	chr9:108458000-108479200	Weak transcription	Fetal Brain Male	brain
14	chr9:108458000-108497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:108458200-108468400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr9:108458200-108468600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr9:108458200-108470600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:108458200-108476400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:108458200-108478800	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:108458200-108480800	Weak transcription	Brain Angular Gyrus	brain
21	chr9:108458200-108491400	Weak transcription	HSMMtube	muscle
22	chr9:108458200-108491600	Weak transcription	Brain Anterior Caudate	brain
23	chr9:108458200-108495400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:108458200-108497000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:108458400-108470200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:108458400-108470400	Weak transcription	Liver	Liver
27	chr9:108458600-108472600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:108458800-108470600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:108459000-108468200	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:108459000-108476000	Weak transcription	Fetal Brain Female	brain
31	chr9:108459200-108468600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr9:108459200-108472400	Weak transcription	Dnd41	blood
33	chr9:108459200-108489400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:108459600-108470200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr9:108461200-108463800	Enhancers	Primary hematopoietic stem cells	blood
36	chr9:108461200-108463800	Enhancers	Fetal Heart	heart
37	chr9:108461400-108464400	Enhancers	Fetal Intestine Large	intestine
38	chr9:108461600-108464400	Enhancers	Fetal Intestine Small	intestine
39	chr9:108461600-108465200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:108462000-108465000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:108462200-108463800	Enhancers	K562	blood
42	chr9:108462400-108464200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr9:108462600-108463200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr9:108462600-108463200	Enhancers	Hela-S3	cervix
45	chr9:108462600-108464200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr9:108462600-108472600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:108462800-108463200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:108462800-108463200	Enhancers	HepG2	liver
49	chr9:108462800-108463400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr9:108462800-108463800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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