Variant report

Variant	rs7039618
Chromosome Location	chr9:108457806-108457807
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	chr9:108455042..108457950-chr9:108472079..108474194,2	K562	blood:
5	chr9:108451729..108454266-chr9:108456840..108459678,2	K562	blood:

Variant related genes	Relation type
ENSG00000186051	Chromatin interaction
ENSG00000228366	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10115634	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10118720	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10119254	0.91[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10512339	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10733555	0.82[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739210	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]
rs10739211	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10739212	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10759127	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759129	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759131	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10816293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10978213	0.82[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10978216	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271247	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271248	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3105993	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[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];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3794486	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]
rs6477461	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7019359	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7026251	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039893	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	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7859253	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7862873	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9299110	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7039618	TMEM38B	cis	lymphoblastoid	seeQTL
rs7039618	TMEM38B	cis	normal skin	skin_eQTL
rs7039618	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL
rs7039618	LPPR1	cis	parietal	SCAN
rs7039618	TAL2	cis	cerebellum	SCAN
rs7039618	OR13C2	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108455600-108458000	Active TSS	Colonic Mucosa	Colon
2	chr9:108455800-108458000	Bivalent/Poised TSS	Fetal Stomach	stomach
3	chr9:108455800-108458000	Active TSS	Right Ventricle	heart
4	chr9:108455800-108458200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:108455800-108458200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:108455800-108458200	Active TSS	Right Atrium	heart
7	chr9:108455800-108459800	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr9:108456000-108458000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr9:108456000-108458000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:108456000-108458000	Active TSS	Aorta	Aorta
11	chr9:108456000-108458000	Active TSS	Brain Cingulate Gyrus	brain
12	chr9:108456000-108458000	Active TSS	Left Ventricle	heart
13	chr9:108456000-108458600	Active TSS	Psoas Muscle	Psoas
14	chr9:108456000-108459200	Active TSS	Fetal Muscle Trunk	muscle
15	chr9:108456200-108458000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:108456200-108458000	Active TSS	Ovary	ovary
17	chr9:108456200-108458200	Active TSS	NHDF-Ad	bronchial
18	chr9:108456200-108458400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr9:108456200-108458400	Active TSS	GM12878-XiMat	blood
20	chr9:108456400-108458000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:108456400-108458000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:108456400-108458000	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr9:108456400-108458000	Active TSS	Fetal Intestine Large	intestine
24	chr9:108456400-108458000	Active TSS	Placenta	Placenta
25	chr9:108456400-108458200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:108456400-108458200	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr9:108456400-108458200	Active TSS	Fetal Intestine Small	intestine
28	chr9:108456400-108458200	Active TSS	HMEC	breast
29	chr9:108456400-108458200	Active TSS	NHLF	lung
30	chr9:108456400-108458200	Active TSS	Osteobl	bone
31	chr9:108456400-108458400	Active TSS	Fetal Brain Female	brain
32	chr9:108456600-108458000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:108456600-108458000	Active TSS	HSMM	muscle
34	chr9:108456600-108458200	Active TSS	HSMMtube	muscle
35	chr9:108456600-108458400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:108456600-108458600	Active TSS	Fetal Muscle Leg	muscle
37	chr9:108457000-108458000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:108457200-108458000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:108457200-108458200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr9:108457200-108458200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:108457400-108458000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
42	chr9:108457400-108458000	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr9:108457400-108458000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr9:108457400-108458000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr9:108457400-108458000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr9:108457400-108458400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:108457400-108458400	Flanking Active TSS	Dnd41	blood
48	chr9:108457600-108458000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:108457600-108458000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
50	chr9:108457600-108458000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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