Variant report

Variant	rs7039893
Chromosome Location	chr9:108458017-108458018
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108423380..108425504-chr9:108456986..108459535,2	MCF-7	breast:
2	chr9:108456828..108459510-chr9:108460242..108461913,3	MCF-7	breast:
3	chr9:108451266..108453229-chr9:108456840..108459511,2	K562	blood:
4	chr9:108451729..108454266-chr9:108456840..108459678,2	K562	blood:

Variant related genes	Relation type
ENSG00000186051	Chromatin interaction

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

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

rs_ID	r²[population]
rs10115634	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10118720	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119254	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10512339	0.82[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10733555	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739209	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739210	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]
rs10739211	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739212	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759127	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10759129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759131	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10816293	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10978213	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10978216	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271247	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271248	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3105993	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3126471	0.86[JPT][hapmap]
rs3793640	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794486	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]
rs6477461	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7019359	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7026251	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7039618	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859125	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7862873	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9299110	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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
rs7039893	TMEM38B	cis	normal skin	skin_eQTL
rs7039893	TMEM38B	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108455800-108458200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr9:108455800-108458200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:108455800-108458200	Active TSS	Right Atrium	heart
4	chr9:108455800-108459800	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr9:108456000-108458600	Active TSS	Psoas Muscle	Psoas
6	chr9:108456000-108459200	Active TSS	Fetal Muscle Trunk	muscle
7	chr9:108456200-108458200	Active TSS	NHDF-Ad	bronchial
8	chr9:108456200-108458400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr9:108456200-108458400	Active TSS	GM12878-XiMat	blood
10	chr9:108456400-108458200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
11	chr9:108456400-108458200	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:108456400-108458200	Active TSS	Fetal Intestine Small	intestine
13	chr9:108456400-108458200	Active TSS	HMEC	breast
14	chr9:108456400-108458200	Active TSS	NHLF	lung
15	chr9:108456400-108458200	Active TSS	Osteobl	bone
16	chr9:108456400-108458400	Active TSS	Fetal Brain Female	brain
17	chr9:108456600-108458200	Active TSS	HSMMtube	muscle
18	chr9:108456600-108458400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr9:108456600-108458600	Active TSS	Fetal Muscle Leg	muscle
20	chr9:108457200-108458200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr9:108457200-108458200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:108457400-108458400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:108457400-108458400	Flanking Active TSS	Dnd41	blood
24	chr9:108457600-108458200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:108457600-108458200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:108457600-108458200	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr9:108457600-108458200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr9:108457600-108458200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:108457600-108458200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr9:108457600-108458200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr9:108457600-108458200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:108457600-108458200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:108457600-108458200	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr9:108457600-108458200	Flanking Active TSS	Fetal Heart	heart
35	chr9:108457600-108458200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr9:108457600-108458200	Flanking Active TSS	Hela-S3	cervix
37	chr9:108457600-108458200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr9:108457600-108458200	Flanking Active TSS	NHEK	skin
39	chr9:108457600-108458400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:108457600-108458600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr9:108457600-108458600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:108457800-108458200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr9:108457800-108458200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr9:108457800-108458200	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr9:108457800-108458200	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr9:108457800-108458400	Flanking Active TSS	HepG2	liver
47	chr9:108457800-108463200	Weak transcription	Small Intestine	intestine
48	chr9:108457800-108472800	Weak transcription	Spleen	Spleen
49	chr9:108457800-108476200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:108457800-108492200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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