Variant report

Variant	rs219230
Chromosome Location	chr7:150941609-150941610
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	IRF1	chr7:150941441-150941757	K562	blood:	n/a	n/a
2	CTCF	chr7:150941460-150941610	HCM	heart:	n/a	chr7:150941560-150941581
3	CTCF	chr7:150941500-150941650	AoAF	blood vessel:	n/a	chr7:150941560-150941581
4	RAD21	chr7:150941281-150941848	HCT-116	colon:	n/a	chr7:150941591-150941603 chr7:150941563-150941582
5	SMC3	chr7:150941379-150941738	GM12878	blood:	n/a	chr7:150941567-150941581
6	CTCF	chr7:150941500-150941650	GM12874	blood:	n/a	chr7:150941560-150941581
7	TCF12	chr7:150941340-150941610	GM12878	blood:	n/a	n/a
8	RAD21	chr7:150941397-150941636	HepG2	liver:	n/a	chr7:150941591-150941603 chr7:150941563-150941582
9	CTCF	chr7:150941224-150941839	K562	blood:	n/a	chr7:150941560-150941581
10	CTCF	chr7:150941199-150941683	GM12892	blood:	n/a	chr7:150941560-150941581
11	SMC3	chr7:150941323-150941775	Hela-S3	cervix:	n/a	chr7:150941567-150941581
12	CTCF	chr7:150941480-150941630	NHEK	skin:	n/a	chr7:150941560-150941581
13	CTCF	chr7:150941460-150941610	HCT-116	colon:	n/a	chr7:150941560-150941581
14	CTCF	chr7:150941500-150941650	HVMF	connective:	n/a	chr7:150941560-150941581
15	CTCF	chr7:150941447-150941685	GM19239	blood:	n/a	chr7:150941560-150941581
16	CTCF	chr7:150941500-150941650	GM12866	blood:	n/a	chr7:150941560-150941581
17	RAD21	chr7:150941212-150941706	H1-hESC	embryonic stem cell:	n/a	chr7:150941591-150941603 chr7:150941563-150941582
18	CTCF	chr7:150941520-150941670	GM12870	blood:	n/a	chr7:150941560-150941581
19	CTCF	chr7:150941470-150941663	H1-hESC	embryonic stem cell:	n/a	chr7:150941560-150941581
20	CTCF	chr7:150941500-150941650	HMF	breast:	n/a	chr7:150941560-150941581
21	MTA3	chr7:150940959-150941740	GM12878	blood:	n/a	n/a
22	CTCF	chr7:150941460-150941610	NHLF	lung:	n/a	chr7:150941560-150941581
23	CTCF	chr7:150941460-150941610	GM12864	blood:	n/a	chr7:150941560-150941581
24	CTCF	chr7:150941500-150941650	HEK293	kidney:	n/a	chr7:150941560-150941581
25	CTCF	chr7:150941520-150941670	AG09309	skin:	n/a	chr7:150941560-150941581
26	STAT5A	chr7:150941357-150941717	GM12878	blood:	n/a	n/a
27	CTCF	chr7:150941480-150941630	GM12875	blood:	n/a	chr7:150941560-150941581
28	CBX3	chr7:150941299-150941783	K562	blood:	n/a	n/a
29	CTCF	chr7:150941458-150941660	MCF-7	breast:	n/a	chr7:150941560-150941581
30	CTCF	chr7:150941520-150941670	HBMEC	blood vessel:	n/a	chr7:150941560-150941581
31	RUNX3	chr7:150941366-150941686	GM12878	blood:	n/a	n/a
32	CTCF	chr7:150941480-150941630	HRPEpiC	eye:	n/a	chr7:150941560-150941581
33	CTCF	chr7:150941500-150941650	AG10803	skin:	n/a	chr7:150941560-150941581
34	CTCF	chr7:150941437-150941718	LNCaP	prostate:	n/a	chr7:150941560-150941581
35	YY1	chr7:150941401-150941742	SK-N-SH_RA	brain:	n/a	n/a
36	CTCF	chr7:150941460-150941610	HRE	kidney:	n/a	chr7:150941560-150941581
37	CTCF	chr7:150941480-150941630	GM12867	blood:	n/a	chr7:150941560-150941581
38	RAD21	chr7:150941357-150941790	ECC-1	luminal epithelium:	n/a	chr7:150941591-150941603 chr7:150941563-150941582
39	CTCF	chr7:150941500-150941650	HAc	cerebellar:	n/a	chr7:150941560-150941581
40	CTCF	chr7:150941520-150941670	HCPEpiC	choroid plexus:	n/a	chr7:150941560-150941581
41	MAZ	chr7:150941466-150941727	HepG2	liver:	n/a	n/a
42	GATA2	chr7:150941398-150942139	SH-SY5Y	brain:	n/a	n/a
43	CTCF	chr7:150941459-150941701	GM20000	blood:	n/a	chr7:150941560-150941581
44	MAX	chr7:150941534-150941618	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr7:150941481-150941688	MCF-7	breast:	n/a	chr7:150941560-150941581
46	CTCF	chr7:150941477-150941711	LNCaP	prostate:	n/a	chr7:150941560-150941581
47	CTCF	chr7:150941500-150941650	GM06990	blood:	n/a	chr7:150941560-150941581
48	POLR2A	chr7:150941340-150941865	SK-N-SH	brain:	n/a	n/a
49	SMC3	chr7:150940796-150943624	SK-N-SH	brain:	n/a	chr7:150941980-150941987 chr7:150941567-150941581 chr7:150941940-150941947
50	CTCF	chr7:150941491-150941673	Fibrobl	skin:	n/a	chr7:150941560-150941581

No.	Distal block	Cell Line	Cell type
1	chr7:150869379..150870234-chr7:150941055..150942048,8	MCF-7	breast:
2	chr7:150888388..150889316-chr7:150941010..150942053,3	K562	blood:
3	chr7:150820799..150821593-chr7:150941510..150942032,2	K562	blood:
4	chr7:150923495..150927436-chr7:150940006..150942925,4	MCF-7	breast:
5	chr7:150820748..150821377-chr7:150941500..150942022,2	MCF-7	breast:
6	chr7:150901645..150902197-chr7:150940945..150941682,2	K562	blood:
7	chr7:150869400..150870347-chr7:150941097..150942121,7	K562	blood:
8	chr7:150938571..150942838-chr7:150950941..150954111,4	MCF-7	breast:
9	chr7:150865018..150866330-chr7:150941109..150942155,6	K562	blood:
10	chr7:150820602..150821298-chr7:150941184..150941993,2	MCF-7	breast:
11	chr7:150819780..150822617-chr7:150940406..150943194,3	MCF-7	breast:
12	chr7:150941406..150944514-chr7:150945051..150947075,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243018	TF binding region
SMARCD3	TF binding region
ENSG00000082014	Chromatin interaction
ENSG00000243018	Chromatin interaction
ENSG00000033050	Chromatin interaction
ENSG00000133612	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12668799	0.84[ASN][1000 genomes]
rs2045465	0.82[ASN][1000 genomes]
rs219229	0.85[ASN][1000 genomes]
rs219233	0.82[ASN][1000 genomes]
rs2252694	0.82[ASN][1000 genomes]
rs2530458	0.93[ASN][1000 genomes]
rs2530459	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2792431	0.82[ASN][1000 genomes]
rs2792433	0.81[ASN][1000 genomes]
rs3789823	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807386	0.82[ASN][1000 genomes]
rs3807387	0.82[ASN][1000 genomes]
rs4236429	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4236430	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472433	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58125572	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6464133	0.81[ASN][1000 genomes]
rs6958591	0.96[ASN][1000 genomes]
rs7786030	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821419	chr7:150593315-150974269	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
2	nsv889476	chr7:150729212-150951819	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	120 gene(s)	inside rSNPs	diseases
3	nsv609035	chr7:150896223-150955765	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv889487	chr7:150922952-150988172	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv889488	chr7:150926775-150955765	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs219230	ABCF2	cis	Thyroid	GTEx
rs219230	ABCF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150931000-150944600	Weak transcription	Fetal Kidney	kidney
2	chr7:150931600-150944400	Weak transcription	Hela-S3	cervix
3	chr7:150932800-150942000	Weak transcription	Psoas Muscle	Psoas
4	chr7:150936400-150942200	Weak transcription	HMEC	breast
5	chr7:150936800-150941800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:150938600-150941800	Weak transcription	NH-A	brain
7	chr7:150939200-150942000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:150939200-150942000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:150939400-150941800	Enhancers	Fetal Brain Male	brain
10	chr7:150939400-150941800	Enhancers	HepG2	liver
11	chr7:150939600-150941800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:150939600-150941800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr7:150939600-150942000	Weak transcription	Aorta	Aorta
14	chr7:150939800-150941800	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr7:150940000-150941800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:150940000-150941800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:150940000-150942200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:150940000-150942200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr7:150940000-150942400	Bivalent Enhancer	Stomach Mucosa	stomach
20	chr7:150940000-150942800	Enhancers	Spleen	Spleen
21	chr7:150940200-150941800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:150940200-150941800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr7:150940200-150941800	Enhancers	Colon Smooth Muscle	Colon
24	chr7:150940200-150942000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr7:150940200-150942000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr7:150940200-150942000	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr7:150940200-150942200	Enhancers	Brain Cingulate Gyrus	brain
28	chr7:150940200-150942200	Flanking Active TSS	Fetal Brain Female	brain
29	chr7:150940200-150942600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr7:150940200-150942600	Enhancers	Lung	lung
31	chr7:150940200-150943000	Enhancers	Adipose Nuclei	Adipose
32	chr7:150940200-150944800	Enhancers	Pancreas	Pancrea
33	chr7:150940200-150945400	Enhancers	K562	blood
34	chr7:150940400-150941800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:150940400-150942000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr7:150940400-150942200	Enhancers	Brain Angular Gyrus	brain
37	chr7:150940400-150942200	Bivalent Enhancer	Colonic Mucosa	Colon
38	chr7:150940400-150942400	Enhancers	Liver	Liver
39	chr7:150940400-150942600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr7:150940400-150944000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:150940600-150942200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr7:150940600-150942600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
43	chr7:150940800-150942000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr7:150940800-150942000	Genic enhancers	HSMM	muscle
45	chr7:150940800-150942200	Enhancers	Brain Substantia Nigra	brain
46	chr7:150940800-150942200	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr7:150940800-150942200	Enhancers	Left Ventricle	heart
48	chr7:150940800-150942400	Bivalent Enhancer	Fetal Intestine Large	intestine
49	chr7:150940800-150942800	Bivalent Enhancer	Fetal Stomach	stomach
50	chr7:150940800-150942800	Weak transcription	Small Intestine	intestine

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