Variant report

Variant	rs2590790
Chromosome Location	chr4:54571562-54571563
allele	C/T
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	GATA3	chr4:54571371-54572883	SK-N-SH	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
2	TCF3	chr4:54571284-54571855	GM12878	blood:	n/a	chr4:54571533-54571546
3	RELA	chr4:54571098-54572151	GM19099	blood:	n/a	n/a
4	SPI1	chr4:54571088-54571979	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr4:54571410-54571656	GM12878	blood:	n/a	n/a
6	GATA3	chr4:54571352-54572953	SK-N-SH	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
7	POLR2A	chr4:54571263-54571799	GM12892	blood:	n/a	n/a
8	RELA	chr4:54570983-54572148	GM12891	blood:	n/a	n/a
9	RUNX3	chr4:54571297-54571909	GM12878	blood:	n/a	n/a
10	CHD2	chr4:54571327-54571635	GM12878	blood:	n/a	n/a
11	ATF2	chr4:54571152-54571797	GM12878	blood:	n/a	n/a
12	RELA	chr4:54571028-54572161	GM18951	blood:	n/a	n/a
13	RELA	chr4:54571255-54571969	GM19193	blood:	n/a	n/a
14	TCF12	chr4:54571314-54571673	GM12878	blood:	n/a	n/a
15	TBP	chr4:54571397-54571918	GM12878	blood:	n/a	n/a
16	IKZF1	chr4:54571181-54572140	GM12878	blood:	n/a	n/a
17	EBF1	chr4:54571308-54571630	GM12878	blood:	n/a	n/a
18	GATA2	chr4:54571496-54572447	HUVEC	blood vessel:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54571704-54571718 chr4:54572402-54572410 chr4:54572323-54572330
19	RUNX3	chr4:54571214-54571914	GM12878	blood:	n/a	n/a
20	RELA	chr4:54571254-54571709	GM15510	blood:	n/a	n/a
21	TCF3	chr4:54571336-54571739	GM12878	blood:	n/a	chr4:54571533-54571546
22	BATF	chr4:54571251-54571588	GM12878	blood:	n/a	n/a
23	EP300	chr4:54571291-54571846	GM12878	blood:	n/a	n/a
24	MTA3	chr4:54571168-54572102	GM12878	blood:	n/a	n/a
25	RELA	chr4:54571061-54572091	GM12878	blood:	n/a	n/a
26	EBF1	chr4:54571283-54571742	GM12878	blood:	n/a	n/a
27	WRNIP1	chr4:54571395-54571936	GM12878	blood:	n/a	n/a
28	BCL11A	chr4:54571331-54571673	GM12878	blood:	n/a	n/a
29	SPI1	chr4:54571322-54571672	GM12891	blood:	n/a	n/a
30	PAX5	chr4:54571192-54571674	GM12878	blood:	n/a	n/a
31	ZNF143	chr4:54571388-54571609	GM12878	blood:	n/a	n/a
32	EBF1	chr4:54570965-54571845	GM12878	blood:	n/a	n/a
33	SPI1	chr4:54571415-54571639	GM12878	blood:	n/a	n/a
34	BATF	chr4:54571258-54571933	GM12878	blood:	n/a	n/a
35	RCOR1	chr4:54571377-54571607	GM12878	blood:	n/a	n/a
36	NFIC	chr4:54570856-54571953	GM12878	blood:	n/a	n/a
37	TCF12	chr4:54571357-54571691	GM12878	blood:	n/a	n/a
38	RELA	chr4:54571181-54571827	GM10847	blood:	n/a	n/a
39	REST	chr4:54571556-54571858	PFSK-1	brain:	n/a	n/a
40	BHLHE40	chr4:54571385-54571609	GM12878	blood:	n/a	n/a
41	EP300	chr4:54571380-54571647	GM12878	blood:	n/a	n/a
42	RELA	chr4:54571217-54572085	GM18505	blood:	n/a	n/a
43	SPI1	chr4:54571368-54571709	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54570474..54572484-chr4:54573853..54575756,2	K562	blood:
2	chr4:54568125..54570977-chr4:54571339..54573651,2	K562	blood:

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1382083	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2245157	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590776	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590828	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590830	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590831	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2590832	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2616394	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616397	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616403	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2616406	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2616408	0.88[EUR][1000 genomes]
rs2616413	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2616414	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59445919	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728586	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73250987	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2590790	Hs.164463	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54569200-54573200	Enhancers	Primary B cells from peripheral blood	blood
2	chr4:54569400-54572400	Weak transcription	Psoas Muscle	Psoas
3	chr4:54569400-54572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:54569400-54573200	Enhancers	Primary B cells from cord blood	blood
5	chr4:54569400-54577200	Weak transcription	Aorta	Aorta
6	chr4:54569600-54572000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:54569600-54572800	Weak transcription	Gastric	stomach
8	chr4:54569600-54572800	Weak transcription	Pancreas	Pancrea
9	chr4:54569600-54573200	Weak transcription	Colonic Mucosa	Colon
10	chr4:54569600-54580200	Weak transcription	HSMM	muscle
11	chr4:54569600-54583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:54569800-54571600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:54569800-54572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:54569800-54572800	Weak transcription	Ovary	ovary
15	chr4:54569800-54572800	Weak transcription	Spleen	Spleen
16	chr4:54569800-54577800	Weak transcription	Right Atrium	heart
17	chr4:54569800-54578600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:54570000-54572200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:54570000-54572400	Weak transcription	Liver	Liver
20	chr4:54570200-54572000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr4:54570200-54572400	Weak transcription	Fetal Heart	heart
22	chr4:54570200-54577800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:54570400-54571600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:54570400-54572000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:54570400-54572600	Weak transcription	Adipose Nuclei	Adipose
26	chr4:54570400-54572800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr4:54570600-54571600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:54570600-54572600	Weak transcription	Fetal Kidney	kidney
29	chr4:54570800-54572200	Enhancers	Lung	lung
30	chr4:54570800-54572600	Flanking Active TSS	GM12878-XiMat	blood
31	chr4:54571000-54573200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:54571200-54571600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:54571200-54571800	Enhancers	NH-A	brain
34	chr4:54571200-54572200	Enhancers	HUVEC	blood vessel
35	chr4:54571200-54572400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:54571200-54572600	Enhancers	A549	lung
37	chr4:54571200-54573200	Enhancers	NHDF-Ad	bronchial
38	chr4:54571400-54571600	Enhancers	Primary hematopoietic stem cells	blood
39	chr4:54571400-54571600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:54571400-54571600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr4:54571400-54572200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr4:54571400-54572200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:54571400-54572600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:54571400-54572600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr4:54571400-54573000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr4:54571400-54573000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr4:54571400-54573000	Enhancers	Osteobl	bone
48	chr4:54571400-54573200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:54571400-54573200	Enhancers	NHLF	lung
50	chr4:54571400-54576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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