Variant report

Variant	rs10412123
Chromosome Location	chr19:51762581-51762582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:51762579-51763042	K562	blood:	n/a	n/a
2	CTCF	chr19:51762406-51763184	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr19:51762489-51763085	MCF-7	breast:	n/a	n/a
4	RAD21	chr19:51762544-51762968	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr19:51762459-51763033	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr19:51762539-51763145	MCF-7	breast:	n/a	n/a
7	RAD21	chr19:51762575-51763049	A549	lung:	n/a	n/a
8	RAD21	chr19:51762574-51763009	GM12878	blood:	n/a	n/a
9	RAD21	chr19:51762438-51763061	HCT-116	colon:	n/a	n/a
10	RAD21	chr19:51762575-51762879	GM12878	blood:	n/a	n/a
11	CTCF	chr19:51762567-51763005	K562	blood:	n/a	n/a
12	RAD21	chr19:51762492-51762979	HepG2	liver:	n/a	n/a
13	RAD21	chr19:51762568-51763002	MCF-7	breast:	n/a	n/a
14	SMC3	chr19:51762570-51762980	GM12878	blood:	n/a	n/a
15	RAD21	chr19:51762554-51762985	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr19:51762508-51763070	MCF-7	breast:	n/a	n/a
17	RAD21	chr19:51762525-51763082	HCT-116	colon:	n/a	n/a
18	RAD21	chr19:51762521-51763032	A549	lung:	n/a	n/a
19	CTCF	chr19:51762460-51762610	AoAF	blood vessel:	n/a	n/a
20	CTCF	chr19:51762455-51763088	HCT-116	colon:	n/a	n/a
21	CTCF	chr19:51762520-51762670	HCM	heart:	n/a	n/a
22	CTCF	chr19:51762443-51763228	A549	lung:	n/a	n/a
23	CTCF	chr19:51762560-51763069	HCT-116	colon:	n/a	n/a
24	SMC3	chr19:51762562-51763410	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr19:51762562-51762956	HepG2	liver:	n/a	n/a
26	RAD21	chr19:51762549-51762887	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51661388..51662622-chr19:51761876..51763512,12	MCF-7	breast:
2	chr19:51661431..51662712-chr19:51761692..51763149,12	K562	blood:
3	chr19:51600353..51600887-chr19:51762311..51762872,2	K562	blood:
4	chr19:51661493..51662394-chr19:51762311..51762910,6	MCF-7	breast:

No data

Variant related genes	Relation type
SIGLECL1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1034521	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10402797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406897	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs10412214	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10414689	1.00[CEU][hapmap]
rs11084061	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084062	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084064	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11672446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12461282	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12461354	0.82[CHB][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1319675	0.88[ASN][1000 genomes]
rs1501447	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501448	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566578	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17801843	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1803254	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34606577	0.88[ASN][1000 genomes]
rs7253831	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7256372	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256512	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73612300	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8103085	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9676731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989502	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989504	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv518134	chr19:51750238-51765953	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1060026	chr19:51751123-51773175	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51759400-51762800	Enhancers	Primary hematopoietic stem cells	blood
2	chr19:51759400-51762800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr19:51761200-51762800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr19:51761400-51762600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:51761800-51762600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr19:51761800-51762800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr19:51761800-51762800	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr19:51761800-51762800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr19:51762000-51762800	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr19:51762000-51762800	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr19:51762200-51762800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr19:51762200-51762800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:51762400-51762600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr19:51762400-51762600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:51762400-51762800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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