Variant report

Variant	rs55719825
Chromosome Location	chr2:11049825-11049826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:11049706-11050179	MCF-7	breast:	n/a	n/a
2	CTCF	chr2:11049529-11050697	A549	lung:	n/a	chr2:11050275-11050283
3	CTCF	chr2:11049791-11050170	K562	blood:	n/a	n/a
4	RAD21	chr2:11049792-11050197	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr2:11049780-11049930	HMEC	breast:	n/a	n/a
6	CTCF	chr2:11049811-11050181	K562	blood:	n/a	n/a
7	CTCF	chr2:11049762-11050170	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr2:11049746-11050231	HCT-116	colon:	n/a	n/a
9	RAD21	chr2:11049774-11050169	HepG2	liver:	n/a	n/a
10	CTCF	chr2:11049809-11050108	A549	lung:	n/a	n/a
11	CTCF	chr2:11049329-11050644	SK-N-SH	brain:	n/a	chr2:11050275-11050283
12	RAD21	chr2:11049777-11050226	A549	lung:	n/a	n/a
13	RAD21	chr2:11049802-11050166	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr2:11049818-11050150	IMR90	lung:	n/a	n/a
15	MAZ	chr2:11049818-11050171	K562	blood:	n/a	n/a
16	CTCF	chr2:11049818-11050180	IMR90	lung:	n/a	n/a
17	RAD21	chr2:11049734-11050080	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr2:11049820-11049970	HCM	heart:	n/a	n/a
19	CTCF	chr2:11049672-11050306	HCT-116	colon:	n/a	chr2:11050275-11050283
20	TCF12	chr2:11049791-11050101	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr2:11049720-11049870	GM12866	blood:	n/a	n/a
22	RAD21	chr2:11049772-11050182	ECC-1	luminal epithelium:	n/a	n/a
23	TCF12	chr2:11049779-11050101	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr2:11049800-11049950	GM06990	blood:	n/a	n/a
25	CTCF	chr2:11049818-11050166	HepG2	liver:	n/a	n/a
26	CTCF	chr2:11049820-11049970	A549	lung:	n/a	n/a
27	CTCF	chr2:11049814-11050097	A549	lung:	n/a	n/a
28	RAD21	chr2:11049734-11050301	A549	lung:	n/a	n/a
29	CTCF	chr2:11049762-11050180	H1-hESC	embryonic stem cell:	n/a	n/a
30	RAD21	chr2:11049756-11050275	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr2:11049820-11049970	GM12864	blood:	n/a	n/a
32	RAD21	chr2:11049730-11050280	HCT-116	colon:	n/a	n/a
33	CTCF	chr2:11049796-11050178	MCF-7	breast:	n/a	n/a
34	RAD21	chr2:11049730-11050215	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11049134..11051684-chr2:11064717..11067313,2	K562	blood:
2	chr2:11049420..11051539-chr2:11073823..11076217,2	MCF-7	breast:
3	chr2:11049631..11050251-chr2:11168175..11168739,2	MCF-7	breast:
4	chr2:11034858..11036763-chr2:11049175..11051034,2	MCF-7	breast:
5	chr2:10972202..10972851-chr2:11049568..11050477,2	MCF-7	breast:

No data

Variant related genes	Relation type
KCNF1	TF binding region
ENSG00000143870	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11901805	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12617163	0.87[ASN][1000 genomes]
rs12623956	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2123483	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4669646	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59786077	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60600332	0.87[AMR][1000 genomes]
rs61193809	0.91[AMR][1000 genomes];0.89[ASN][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	nsv580969	chr2:11033567-11081645	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv873662	chr2:11035430-11061156	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
3	nsv521177	chr2:11040146-11066699	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11044800-11050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:11045000-11051200	Weak transcription	Right Ventricle	heart
3	chr2:11049000-11050400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:11049000-11051400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:11049200-11051400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:11049400-11050400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:11049400-11050400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:11049400-11050600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr2:11049400-11051000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:11049600-11050600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:11049600-11050600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:11049600-11050800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr2:11049800-11051000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:11049800-11051600	Enhancers	Cortex derived primary cultured neurospheres	brain

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