Variant report

Variant	rs17083333
Chromosome Location	chr4:54572066-54572067
allele	G/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	RELA	chr4:54571098-54572151	GM19099	blood:	n/a	n/a
3	SMC3	chr4:54571994-54573067	GM12878	blood:	n/a	chr4:54572777-54572791
4	GATA3	chr4:54571352-54572953	SK-N-SH	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
5	CTCF	chr4:54572009-54573461	SK-N-SH	brain:	n/a	chr4:54572778-54572791 chr4:54572777-54572798 chr4:54572775-54572793
6	RELA	chr4:54570983-54572148	GM12891	blood:	n/a	n/a
7	RELA	chr4:54571028-54572161	GM18951	blood:	n/a	n/a
8	RAD21	chr4:54572043-54573279	SK-N-SH	brain:	n/a	chr4:54572776-54572795
9	SMC3	chr4:54571979-54573408	SK-N-SH	brain:	n/a	chr4:54572777-54572791
10	IKZF1	chr4:54571181-54572140	GM12878	blood:	n/a	n/a
11	CTCF	chr4:54572000-54572150	HCPEpiC	choroid plexus:	n/a	n/a
12	GATA2	chr4:54571496-54572447	HUVEC	blood vessel:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54571704-54571718 chr4:54572402-54572410 chr4:54572323-54572330
13	MTA3	chr4:54571168-54572102	GM12878	blood:	n/a	n/a
14	RELA	chr4:54571061-54572091	GM12878	blood:	n/a	n/a
15	RAD21	chr4:54572015-54572391	SK-N-SH_RA	brain:	n/a	n/a
16	CTCF	chr4:54572020-54572170	GM12873	blood:	n/a	n/a
17	RELA	chr4:54571217-54572085	GM18505	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

rs_ID	r²[population]
rs10014722	0.97[ASN][1000 genomes]
rs2590785	0.81[ASN][1000 genomes]
rs2590787	0.81[ASN][1000 genomes]
rs2590789	0.82[ASN][1000 genomes]
rs2616391	0.82[ASN][1000 genomes]
rs2616393	0.82[ASN][1000 genomes]
rs2668538	0.82[ASN][1000 genomes]
rs3947804	0.82[ASN][1000 genomes]
rs715155	0.82[ASN][1000 genomes]

Chromatin state (count:46 , 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	chr4:54569600-54572800	Weak transcription	Gastric	stomach
7	chr4:54569600-54572800	Weak transcription	Pancreas	Pancrea
8	chr4:54569600-54573200	Weak transcription	Colonic Mucosa	Colon
9	chr4:54569600-54580200	Weak transcription	HSMM	muscle
10	chr4:54569600-54583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:54569800-54572800	Weak transcription	Ovary	ovary
12	chr4:54569800-54572800	Weak transcription	Spleen	Spleen
13	chr4:54569800-54577800	Weak transcription	Right Atrium	heart
14	chr4:54569800-54578600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr4:54570000-54572200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:54570000-54572400	Weak transcription	Liver	Liver
17	chr4:54570200-54572400	Weak transcription	Fetal Heart	heart
18	chr4:54570200-54577800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:54570400-54572600	Weak transcription	Adipose Nuclei	Adipose
20	chr4:54570400-54572800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:54570600-54572600	Weak transcription	Fetal Kidney	kidney
22	chr4:54570800-54572200	Enhancers	Lung	lung
23	chr4:54570800-54572600	Flanking Active TSS	GM12878-XiMat	blood
24	chr4:54571000-54573200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:54571200-54572200	Enhancers	HUVEC	blood vessel
26	chr4:54571200-54572400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:54571200-54572600	Enhancers	A549	lung
28	chr4:54571200-54573200	Enhancers	NHDF-Ad	bronchial
29	chr4:54571400-54572200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:54571400-54572200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:54571400-54572600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:54571400-54572600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr4:54571400-54573000	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr4:54571400-54573000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr4:54571400-54573000	Enhancers	Osteobl	bone
36	chr4:54571400-54573200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:54571400-54573200	Enhancers	NHLF	lung
38	chr4:54571400-54576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:54571600-54572200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:54571600-54573200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr4:54571600-54573800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:54572000-54572200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr4:54572000-54572200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr4:54572000-54573000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:54572000-54573000	Bivalent Enhancer	Fetal Lung	lung
46	chr4:54572000-54573000	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links