Variant report

Variant	rs1623888
Chromosome Location	chr12:44711695-44711696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:44711680-44711830	GM12871	blood:	n/a	n/a
2	CTCF	chr12:44711399-44711803	LNCaP	prostate:	n/a	n/a
3	SMC3	chr12:44711339-44711722	GM12878	blood:	n/a	n/a
4	RAD21	chr12:44711320-44711864	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr12:44711640-44711790	HEK293	kidney:	n/a	n/a
6	RAD21	chr12:44711236-44711806	HCT-116	colon:	n/a	n/a
7	CTCF	chr12:44711386-44711801	MCF-7	breast:	n/a	n/a
8	RAD21	chr12:44711351-44711902	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr12:44711389-44711783	MCF-7	breast:	n/a	n/a
10	RAD21	chr12:44711364-44711829	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:44711671-44711729	MCF-7	breast:	n/a	n/a
12	CTCF	chr12:44711680-44711830	HCFaa	heart:	n/a	n/a
13	CTCF	chr12:44711416-44711760	A549	lung:	n/a	n/a
14	CTCF	chr12:44711411-44711849	MCF-7	breast:	n/a	n/a
15	RAD21	chr12:44711311-44711822	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr12:44711634-44711841	MCF-7	breast:	n/a	n/a
17	RAD21	chr12:44711152-44711964	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr12:44711319-44711819	GM12878	blood:	n/a	n/a
19	CTCF	chr12:44711308-44712219	SK-N-SH	brain:	n/a	n/a
20	RAD21	chr12:44711361-44711713	HepG2	liver:	n/a	n/a
21	RAD21	chr12:44711311-44711729	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr12:44711408-44711760	GM12891	blood:	n/a	n/a
23	RAD21	chr12:44711325-44711712	GM12878	blood:	n/a	n/a
24	RAD21	chr12:44711307-44711773	SK-N-SH_RA	brain:	n/a	n/a
25	CTCF	chr12:44711376-44711815	GM19238	blood:	n/a	n/a
26	CTCF	chr12:44711619-44711821	MCF-7	breast:	n/a	n/a
27	RAD21	chr12:44711301-44711957	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOXP2	chr12:44711451-44711701	SK-N-MC	brain:	n/a	n/a
29	CTCF	chr12:44711318-44711818	HCT-116	colon:	n/a	n/a
30	CTCF	chr12:44711385-44711872	GM12892	blood:	n/a	n/a
31	CTCF	chr12:44711313-44711718	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr12:44711352-44711729	A549	lung:	n/a	n/a
33	RAD21	chr12:44711355-44711828	ECC-1	luminal epithelium:	n/a	n/a
34	CTCF	chr12:44711234-44711910	A549	lung:	n/a	n/a
35	RAD21	chr12:44711386-44711754	HCT-116	colon:	n/a	n/a
36	POLR2A	chr12:44711652-44711848	MCF-7	breast:	n/a	n/a
37	CTCF	chr12:44711349-44711831	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMC3	chr12:44711185-44711990	SK-N-SH	brain:	n/a	n/a
39	CTCF	chr12:44711384-44711846	Fibrobl	skin:	n/a	n/a
40	SMC3	chr12:44711367-44711716	HepG2	liver:	n/a	n/a
41	CTCF	chr12:44711409-44711796	MCF-7	breast:	n/a	n/a
42	RAD21	chr12:44711333-44711750	A549	lung:	n/a	n/a
43	RUNX3	chr12:44711306-44711705	GM12878	blood:	n/a	n/a
44	CTCF	chr12:44711385-44711809	MCF-7	breast:	n/a	n/a
45	CTCF	chr12:44711657-44711810	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr12:44711367-44711820	MCF-7	breast:	n/a	n/a

No data

Variant related genes	Relation type
TMEM117	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1104356	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1612439	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1627100	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17094468	1.00[AMR][1000 genomes]
rs1798019	1.00[AMR][1000 genomes]
rs1798029	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1798030	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1798034	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55885620	1.00[AMR][1000 genomes]
rs56041151	1.00[AMR][1000 genomes]
rs56147425	1.00[AMR][1000 genomes]
rs56341304	1.00[AMR][1000 genomes]
rs56888768	1.00[AMR][1000 genomes]
rs57189846	1.00[AMR][1000 genomes]
rs58093009	1.00[AMR][1000 genomes]
rs58264920	1.00[AMR][1000 genomes]
rs58491255	1.00[AMR][1000 genomes]
rs74085005	1.00[AMR][1000 genomes]
rs74085118	1.00[AMR][1000 genomes]
rs74087507	1.00[AMR][1000 genomes]
rs74087508	1.00[AMR][1000 genomes]
rs74087522	1.00[AMR][1000 genomes]
rs840763	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1038498	chr12:44679455-44816572	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv520635	chr12:44707667-44720874	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44699000-44712600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:44699000-44713800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:44699000-44736000	Weak transcription	Pancreas	Pancrea
4	chr12:44699000-44782000	Weak transcription	Aorta	Aorta
5	chr12:44703400-44711800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:44706800-44711800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:44709200-44743200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:44711600-44711800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:44711600-44712000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:44711600-44712800	Enhancers	Esophagus	oesophagus

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