Variant report

Variant	rs2271248
Chromosome Location	chr9:108456726-108456727
allele	C/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	UBTF	chr9:108455960-108457858	K562	blood:	n/a	n/a
2	MAX	chr9:108456157-108457795	K562	blood:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
3	TFAP2C	chr9:108456387-108457005	Hela-S3	cervix:	n/a	n/a
4	YY1	chr9:108456676-108457434	GM12892	blood:	n/a	chr9:108456791-108456800 chr9:108456789-108456803 chr9:108456845-108456859 chr9:108457064-108457078 chr9:108456767-108456781
5	YY1	chr9:108456612-108457547	K562	blood:	n/a	chr9:108456791-108456800 chr9:108456789-108456803 chr9:108456845-108456859 chr9:108457064-108457078 chr9:108456767-108456781
6	MAX	chr9:108456435-108457941	HCT-116	colon:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
7	POLR2A	chr9:108456663-108457114	Hela-S3	cervix:	n/a	n/a
8	MAX	chr9:108456095-108457003	H1-hESC	embryonic stem cell:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
9	POLR2A	chr9:108456672-108457127	A549	lung:	n/a	n/a
10	BACH1	chr9:108456657-108457053	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr9:108456487-108457079	MCF10A-Er-Src	breast:	n/a	n/a
12	ZBTB7A	chr9:108456623-108457524	K562	blood:	n/a	chr9:108456929-108456940 chr9:108456930-108456941
13	HCFC1	chr9:108456717-108457992	K562	blood:	n/a	n/a
14	TAF1	chr9:108456667-108456955	Hela-S3	cervix:	n/a	n/a
15	E2F6	chr9:108456595-108456930	K562	blood:	n/a	chr9:108456831-108456840 chr9:108456791-108456800 chr9:108456905-108456915 chr9:108456812-108456821
16	POLR2A	chr9:108456567-108457750	K562	blood:	n/a	n/a
17	BHLHE40	chr9:108456181-108457834	GM12878	blood:	n/a	chr9:108456845-108456861
18	E2F4	chr9:108456608-108457646	K562	blood:	n/a	chr9:108456831-108456840 chr9:108456791-108456800 chr9:108456905-108456915 chr9:108456812-108456821
19	MAZ	chr9:108456685-108456979	HepG2	liver:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
20	POLR2A	chr9:108456560-108457534	MCF-7	breast:	n/a	n/a
21	POLR2A	chr9:108456589-108457124	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr9:108456518-108457092	K562	blood:	n/a	n/a
23	YY1	chr9:108456641-108457770	K562	blood:	n/a	chr9:108456791-108456800 chr9:108456789-108456803 chr9:108456845-108456859 chr9:108457064-108457078 chr9:108456767-108456781
24	TBP	chr9:108456345-108457004	H1-hESC	embryonic stem cell:	n/a	n/a
25	PAX5	chr9:108456665-108457051	GM12892	blood:	n/a	chr9:108456812-108456821 chr9:108456883-108456892
26	ETS1	chr9:108456703-108457614	K562	blood:	n/a	chr9:108456791-108456802
27	MAX	chr9:108455825-108458032	NB4	blood:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
28	MAX	chr9:108456581-108457766	HepG2	liver:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
29	MAZ	chr9:108455831-108458053	K562	blood:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
30	POLR2A	chr9:108456621-108457578	GM15510	blood:	n/a	n/a
31	ZNF263	chr9:108456692-108457626	K562	blood:	n/a	n/a
32	TAF7	chr9:108456495-108456800	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr9:108456603-108457176	GM12891	blood:	n/a	chr9:108456791-108456800 chr9:108456789-108456803 chr9:108456845-108456859 chr9:108457064-108457078 chr9:108456767-108456781
34	E2F6	chr9:108456572-108456974	K562	blood:	n/a	chr9:108456831-108456840 chr9:108456791-108456800 chr9:108456905-108456915 chr9:108456812-108456821
35	POLR2A	chr9:108456102-108457855	GM18505	blood:	n/a	n/a
36	RUNX3	chr9:108456716-108457859	GM12878	blood:	n/a	chr9:108456915-108456932
37	POLR2A	chr9:108456674-108457074	MCF10A-Er-Src	breast:	n/a	n/a
38	CTBP2	chr9:108456668-108457712	H1-hESC	embryonic stem cell:	n/a	n/a
39	STAT1	chr9:108456386-108456782	GM12878	blood:	n/a	n/a
40	POLR2A	chr9:108456663-108457362	ProgFib	skin:	n/a	n/a
41	MYC	chr9:108456724-108457876	K562	blood:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
42	HA-E2F1	chr9:108455848-108457785	MCF-7	breast:	n/a	chr9:108455902-108455909 chr9:108456773-108456784 chr9:108456831-108456840 chr9:108456791-108456800 chr9:108455902-108455909 chr9:108456905-108456915 chr9:108455902-108455909 chr9:108456812-108456821
43	RCOR1	chr9:108456571-108457854	HepG2	liver:	n/a	n/a
44	POLR2A	chr9:108456461-108457122	H1-neurons	neurons:	n/a	n/a
45	MXI1	chr9:108456350-108458042	K562	blood:	n/a	n/a
46	EGR1	chr9:108456620-108456961	K562	blood:	n/a	chr9:108456789-108456803 chr9:108456740-108456755 chr9:108456740-108456750 chr9:108456790-108456800 chr9:108456792-108456805 chr9:108456741-108456754 chr9:108456812-108456821 chr9:108456792-108456805 chr9:108456739-108456749
47	MAX	chr9:108456602-108457863	H1-hESC	embryonic stem cell:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
48	IRF1	chr9:108456436-108457013	K562	blood:	n/a	chr9:108456736-108456750 chr9:108456787-108456801
49	MYC	chr9:108456523-108456991	H1-hESC	embryonic stem cell:	n/a	chr9:108456792-108456802 chr9:108456739-108456749
50	E2F4	chr9:108456554-108457010	Hela-S3	cervix:	n/a	chr9:108456831-108456840 chr9:108456791-108456800 chr9:108456905-108456915 chr9:108456812-108456821

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:90102816..90103647-chr9:108456510..108457269,2	NB4	blood:
2	chr9:108455042..108457950-chr9:108472079..108474194,2	K562	blood:

Variant related genes	Relation type
TMEM38B	TF binding region
ENSG00000070961	Chromatin interaction
ENSG00000228366	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10115634	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10118720	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119254	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10512339	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10733555	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10739209	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739210	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739211	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10739212	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759127	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759129	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10759131	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10816293	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10978213	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10978216	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271247	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3105993	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3793640	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794486	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6477461	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7019359	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7026251	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7039618	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7039893	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7859125	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7859253	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7862873	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9299110	0.84[EUR][1000 genomes];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2271248	TMEM38B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108455400-108456800	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:108455400-108456800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:108455400-108457800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:108455600-108458000	Active TSS	Colonic Mucosa	Colon
5	chr9:108455800-108457600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr9:108455800-108457800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr9:108455800-108458000	Bivalent/Poised TSS	Fetal Stomach	stomach
8	chr9:108455800-108458000	Active TSS	Right Ventricle	heart
9	chr9:108455800-108458200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr9:108455800-108458200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:108455800-108458200	Active TSS	Right Atrium	heart
12	chr9:108455800-108459800	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr9:108456000-108457600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:108456000-108457600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:108456000-108457600	Active TSS	Pancreas	Pancrea
16	chr9:108456000-108457800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:108456000-108457800	Active TSS	Gastric	stomach
18	chr9:108456000-108458000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr9:108456000-108458000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:108456000-108458000	Active TSS	Aorta	Aorta
21	chr9:108456000-108458000	Active TSS	Brain Cingulate Gyrus	brain
22	chr9:108456000-108458000	Active TSS	Left Ventricle	heart
23	chr9:108456000-108458600	Active TSS	Psoas Muscle	Psoas
24	chr9:108456000-108459200	Active TSS	Fetal Muscle Trunk	muscle
25	chr9:108456200-108456800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:108456200-108456800	Weak transcription	Spleen	Spleen
27	chr9:108456200-108457200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:108456200-108457800	Active TSS	Esophagus	oesophagus
29	chr9:108456200-108457800	Active TSS	Stomach Mucosa	stomach
30	chr9:108456200-108457800	Active TSS	A549	lung
31	chr9:108456200-108458000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:108456200-108458000	Active TSS	Ovary	ovary
33	chr9:108456200-108458200	Active TSS	NHDF-Ad	bronchial
34	chr9:108456200-108458400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr9:108456200-108458400	Active TSS	GM12878-XiMat	blood
36	chr9:108456400-108456800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:108456400-108457200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:108456400-108457400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr9:108456400-108457400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:108456400-108457400	Active TSS	Primary T cells fromperipheralblood	blood
41	chr9:108456400-108457400	Active TSS	Fetal Thymus	thymus
42	chr9:108456400-108457400	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr9:108456400-108457600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:108456400-108457600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:108456400-108457600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
46	chr9:108456400-108457600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr9:108456400-108457600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:108456400-108457600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:108456400-108457600	Active TSS	Primary B cells from peripheral blood	blood
50	chr9:108456400-108457600	Active TSS	Primary hematopoietic stem cells short term culture	blood

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