Variant report

Variant	rs715155
Chromosome Location	chr4:54572307-54572308
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	SMC3	chr4:54571994-54573067	GM12878	blood:	n/a	chr4:54572777-54572791
3	GATA3	chr4:54571352-54572953	SK-N-SH	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
4	CTCF	chr4:54572009-54573461	SK-N-SH	brain:	n/a	chr4:54572778-54572791 chr4:54572777-54572798 chr4:54572775-54572793
5	CTCF	chr4:54572160-54572310	HRPEpiC	eye:	n/a	n/a
6	RAD21	chr4:54572043-54573279	SK-N-SH	brain:	n/a	chr4:54572776-54572795
7	SMC3	chr4:54571979-54573408	SK-N-SH	brain:	n/a	chr4:54572777-54572791
8	GATA2	chr4:54571496-54572447	HUVEC	blood vessel:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54571704-54571718 chr4:54572402-54572410 chr4:54572323-54572330
9	CTCF	chr4:54572260-54572410	RPTEC	kidney:	n/a	n/a
10	GATA3	chr4:54572136-54572489	T-47D	breast:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330
11	RAD21	chr4:54572015-54572391	SK-N-SH_RA	brain:	n/a	n/a
12	CTCF	chr4:54572220-54572370	SK-N-SH_RA	brain:	n/a	n/a
13	CTCF	chr4:54572180-54572330	GM12873	blood:	n/a	n/a
14	WRNIP1	chr4:54572224-54573063	GM12878	blood:	n/a	n/a
15	CTCF	chr4:54572180-54572330	HBMEC	blood vessel:	n/a	n/a
16	CTCF	chr4:54572160-54572310	HPAF	blood vessel:	n/a	n/a
17	CTCF	chr4:54572280-54572430	AoAF	blood vessel:	n/a	n/a
18	CTCF	chr4:54572160-54572310	AoAF	blood vessel:	n/a	n/a
19	GATA3	chr4:54572202-54572425	SH-SY5Y	brain:	n/a	chr4:54572323-54572330 chr4:54572323-54572330 chr4:54572402-54572410 chr4:54572323-54572330

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: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1551880	0.86[EUR][1000 genomes]
rs17083333	0.82[ASN][1000 genomes]
rs2590785	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2590787	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2590789	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590791	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2590792	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2616391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616393	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668537	0.85[GIH][hapmap]
rs2668538	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

No data

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	chr4:54570000-54572400	Weak transcription	Liver	Liver
16	chr4:54570200-54572400	Weak transcription	Fetal Heart	heart
17	chr4:54570200-54577800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:54570400-54572600	Weak transcription	Adipose Nuclei	Adipose
19	chr4:54570400-54572800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:54570600-54572600	Weak transcription	Fetal Kidney	kidney
21	chr4:54570800-54572600	Flanking Active TSS	GM12878-XiMat	blood
22	chr4:54571000-54573200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:54571200-54572400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:54571200-54572600	Enhancers	A549	lung
25	chr4:54571200-54573200	Enhancers	NHDF-Ad	bronchial
26	chr4:54571400-54572600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:54571400-54572600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr4:54571400-54573000	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr4:54571400-54573000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr4:54571400-54573000	Enhancers	Osteobl	bone
31	chr4:54571400-54573200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:54571400-54573200	Enhancers	NHLF	lung
33	chr4:54571400-54576000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:54571600-54573200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr4:54571600-54573800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:54572000-54573000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:54572000-54573000	Bivalent Enhancer	Fetal Lung	lung
38	chr4:54572000-54573000	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr4:54572200-54572400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:54572200-54572400	Enhancers	Fetal Muscle Trunk	muscle
41	chr4:54572200-54572600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:54572200-54572600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:54572200-54572800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:54572200-54573200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:54572200-54573200	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr4:54572200-54577200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links