Variant report

Variant	rs2590789
Chromosome Location	chr4:54571630-54571631
allele	A/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	GATA3	chr4:54571371-54572883	SK-N-SH	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
2	GATA2	chr4:54571605-54571913	SH-SY5Y	brain:	n/a	chr4:54571704-54571718
3	TCF3	chr4:54571284-54571855	GM12878	blood:	n/a	chr4:54571533-54571546
4	RELA	chr4:54571098-54572151	GM19099	blood:	n/a	n/a
5	SPI1	chr4:54571088-54571979	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr4:54571410-54571656	GM12878	blood:	n/a	n/a
7	GATA3	chr4:54571352-54572953	SK-N-SH	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
8	POLR2A	chr4:54571263-54571799	GM12892	blood:	n/a	n/a
9	RELA	chr4:54570983-54572148	GM12891	blood:	n/a	n/a
10	RUNX3	chr4:54571297-54571909	GM12878	blood:	n/a	n/a
11	CHD2	chr4:54571327-54571635	GM12878	blood:	n/a	n/a
12	ATF2	chr4:54571152-54571797	GM12878	blood:	n/a	n/a
13	RELA	chr4:54571028-54572161	GM18951	blood:	n/a	n/a
14	RELA	chr4:54571255-54571969	GM19193	blood:	n/a	n/a
15	TCF12	chr4:54571314-54571673	GM12878	blood:	n/a	n/a
16	TBP	chr4:54571397-54571918	GM12878	blood:	n/a	n/a
17	IKZF1	chr4:54571181-54572140	GM12878	blood:	n/a	n/a
18	EBF1	chr4:54571308-54571630	GM12878	blood:	n/a	n/a
19	GATA2	chr4:54571496-54572447	HUVEC	blood vessel:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54571704-54571718 chr4:54572402-54572410 chr4:54572323-54572330
20	RUNX3	chr4:54571214-54571914	GM12878	blood:	n/a	n/a
21	RELA	chr4:54571254-54571709	GM15510	blood:	n/a	n/a
22	TCF3	chr4:54571336-54571739	GM12878	blood:	n/a	chr4:54571533-54571546
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	NFYB	chr4:54571575-54571871	GM12878	blood:	n/a	n/a
29	BCL11A	chr4:54571331-54571673	GM12878	blood:	n/a	n/a
30	SPI1	chr4:54571322-54571672	GM12891	blood:	n/a	n/a
31	PAX5	chr4:54571192-54571674	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	NFIC	chr4:54570856-54571953	GM12878	blood:	n/a	n/a
36	TCF12	chr4:54571357-54571691	GM12878	blood:	n/a	n/a
37	RELA	chr4:54571181-54571827	GM10847	blood:	n/a	n/a
38	REST	chr4:54571556-54571858	PFSK-1	brain:	n/a	n/a
39	EP300	chr4:54571380-54571647	GM12878	blood:	n/a	n/a
40	RELA	chr4:54571217-54572085	GM18505	blood:	n/a	n/a
41	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: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1551880	0.88[EUR][1000 genomes]
rs17083333	0.82[ASN][1000 genomes]
rs2590785	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2590787	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2590791	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590792	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2616391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668538	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

No data

Chromatin state (count:47 , 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	chr4:54569800-54572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:54569800-54572800	Weak transcription	Ovary	ovary
14	chr4:54569800-54572800	Weak transcription	Spleen	Spleen
15	chr4:54569800-54577800	Weak transcription	Right Atrium	heart
16	chr4:54569800-54578600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:54570000-54572200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:54570000-54572400	Weak transcription	Liver	Liver
19	chr4:54570200-54572000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr4:54570200-54572400	Weak transcription	Fetal Heart	heart
21	chr4:54570200-54577800	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr4:54570400-54572000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:54570400-54572600	Weak transcription	Adipose Nuclei	Adipose
24	chr4:54570400-54572800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:54570600-54572600	Weak transcription	Fetal Kidney	kidney
26	chr4:54570800-54572200	Enhancers	Lung	lung
27	chr4:54570800-54572600	Flanking Active TSS	GM12878-XiMat	blood
28	chr4:54571000-54573200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:54571200-54571800	Enhancers	NH-A	brain
30	chr4:54571200-54572200	Enhancers	HUVEC	blood vessel
31	chr4:54571200-54572400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:54571200-54572600	Enhancers	A549	lung
33	chr4:54571200-54573200	Enhancers	NHDF-Ad	bronchial
34	chr4:54571400-54572200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr4:54571400-54572200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:54571400-54572600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:54571400-54572600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr4:54571400-54573000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr4:54571400-54573000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:54571400-54573000	Enhancers	Osteobl	bone
41	chr4:54571400-54573200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:54571400-54573200	Enhancers	NHLF	lung
43	chr4:54571400-54576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:54571600-54571800	Enhancers	Small Intestine	intestine
45	chr4:54571600-54572200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:54571600-54573200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr4:54571600-54573800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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