Variant report

Variant	rs2271247
Chromosome Location	chr9:108456888-108456889
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108456828..108459510-chr9:108460242..108461913,3	MCF-7	breast:
2	chr12:90102816..90103647-chr9:108456510..108457269,2	NB4	blood:
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
ENSG00000228366	Chromatin interaction
ENSG00000070961	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10115634	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10118720	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119254	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10512339	0.86[CEU][hapmap];0.86[ASN][1000 genomes]
rs10733555	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739209	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739210	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739211	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739212	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10759127	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10759129	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10759131	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10816293	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10978213	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10978216	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271248	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3105993	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3793640	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794486	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6477461	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7019359	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7026251	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7039618	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7039893	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7859125	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7859253	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7862873	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9299110	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[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
rs2271247	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL
rs2271247	TMEM38B	cis	normal skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108455400-108457800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr9:108455600-108458000	Active TSS	Colonic Mucosa	Colon
3	chr9:108455800-108457600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
4	chr9:108455800-108457800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr9:108455800-108458000	Bivalent/Poised TSS	Fetal Stomach	stomach
6	chr9:108455800-108458000	Active TSS	Right Ventricle	heart
7	chr9:108455800-108458200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:108455800-108458200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:108455800-108458200	Active TSS	Right Atrium	heart
10	chr9:108455800-108459800	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr9:108456000-108457600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:108456000-108457600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:108456000-108457600	Active TSS	Pancreas	Pancrea
14	chr9:108456000-108457800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:108456000-108457800	Active TSS	Gastric	stomach
16	chr9:108456000-108458000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
17	chr9:108456000-108458000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:108456000-108458000	Active TSS	Aorta	Aorta
19	chr9:108456000-108458000	Active TSS	Brain Cingulate Gyrus	brain
20	chr9:108456000-108458000	Active TSS	Left Ventricle	heart
21	chr9:108456000-108458600	Active TSS	Psoas Muscle	Psoas
22	chr9:108456000-108459200	Active TSS	Fetal Muscle Trunk	muscle
23	chr9:108456200-108457200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:108456200-108457800	Active TSS	Esophagus	oesophagus
25	chr9:108456200-108457800	Active TSS	Stomach Mucosa	stomach
26	chr9:108456200-108457800	Active TSS	A549	lung
27	chr9:108456200-108458000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:108456200-108458000	Active TSS	Ovary	ovary
29	chr9:108456200-108458200	Active TSS	NHDF-Ad	bronchial
30	chr9:108456200-108458400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr9:108456200-108458400	Active TSS	GM12878-XiMat	blood
32	chr9:108456400-108457200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:108456400-108457400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr9:108456400-108457400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:108456400-108457400	Active TSS	Primary T cells fromperipheralblood	blood
36	chr9:108456400-108457400	Active TSS	Fetal Thymus	thymus
37	chr9:108456400-108457400	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr9:108456400-108457600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:108456400-108457600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:108456400-108457600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr9:108456400-108457600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
42	chr9:108456400-108457600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:108456400-108457600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr9:108456400-108457600	Active TSS	Primary B cells from peripheral blood	blood
45	chr9:108456400-108457600	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr9:108456400-108457600	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr9:108456400-108457600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr9:108456400-108457600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr9:108456400-108457600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:108456400-108457600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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