Variant report

Variant	rs2678907
Chromosome Location	chr2:58133522-58133523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:183)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:183 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:58133266-58133670	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr2:58133420-58133570	GM12872	blood:	n/a	n/a
3	RAD21	chr2:58133296-58133651	K562	blood:	n/a	n/a
4	CTCF	chr2:58133400-58133550	BE2_C	brain:	n/a	n/a
5	CTCF	chr2:58133335-58133602	Pancreas_OC	pancreas:	n/a	n/a
6	CTCF	chr2:58133342-58133581	GM13977	blood:	n/a	n/a
7	CTCF	chr2:58133460-58133610	NB4	blood:	n/a	n/a
8	CTCF	chr2:58133400-58133550	HepG2	liver:	n/a	n/a
9	RAD21	chr2:58133051-58133863	A549	lung:	n/a	n/a
10	CTCF	chr2:58133351-58133584	LNCaP	prostate:	n/a	n/a
11	CTCF	chr2:58133420-58133570	GM12873	blood:	n/a	n/a
12	RAD21	chr2:58133313-58133569	K562	blood:	n/a	n/a
13	CTCF	chr2:58133317-58133548	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr2:58133400-58133550	HMEC	breast:	n/a	n/a
15	CTCF	chr2:58133400-58133550	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr2:58133400-58133550	HCPEpiC	choroid plexus:	n/a	n/a
17	CTCF	chr2:58133406-58133540	Fibrobl	skin:	n/a	n/a
18	ZNF143	chr2:58133278-58133655	GM12878	blood:	n/a	n/a
19	RFX5	chr2:58133321-58133684	Hela-S3	cervix:	n/a	n/a
20	MYC	chr2:58133298-58133584	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr2:58133400-58133550	Caco-2	colon:	n/a	n/a
22	CTCF	chr2:58133460-58133610	GM12868	blood:	n/a	n/a
23	CTCF	chr2:58133400-58133550	HL-60	blood:	n/a	n/a
24	ZNF143	chr2:58133287-58133618	K562	blood:	n/a	n/a
25	RAD21	chr2:58133194-58133743	HepG2	liver:	n/a	n/a
26	RAD21	chr2:58133252-58133635	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr2:58133380-58133530	AG09319	gingival:	n/a	n/a
28	CTCF	chr2:58133337-58133575	GM10266	blood:	n/a	n/a
29	RAD21	chr2:58133260-58133673	HepG2	liver:	n/a	n/a
30	SMC3	chr2:58133195-58133908	GM12878	blood:	n/a	n/a
31	TAL1	chr2:58133233-58133525	K562	blood:	n/a	n/a
32	CTCF	chr2:58133400-58133550	HCFaa	heart:	n/a	n/a
33	TEAD4	chr2:58133373-58133681	ECC-1	luminal epithelium:	n/a	chr2:58133508-58133517
34	CTCF	chr2:58133380-58133530	WI-38	lung:	n/a	n/a
35	CTCF	chr2:58133271-58133944	SK-N-SH	brain:	n/a	n/a
36	RAD21	chr2:58133199-58133692	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr2:58133380-58133530	AG09309	skin:	n/a	n/a
38	CTCF	chr2:58133380-58133530	HA-sp	spinal cord:	n/a	n/a
39	JUND	chr2:58133374-58133752	K562	blood:	n/a	n/a
40	CTCF	chr2:58133400-58133550	AG10803	skin:	n/a	n/a
41	TEAD4	chr2:58133266-58133672	H1-hESC	embryonic stem cell:	n/a	chr2:58133508-58133517
42	CTCF	chr2:58133400-58133550	HBMEC	blood vessel:	n/a	n/a
43	CTCF	chr2:58133380-58133530	AG04449	skin:	n/a	n/a
44	CTCF	chr2:58133400-58133550	GM12875	blood:	n/a	n/a
45	CTCF	chr2:58133400-58133550	HEK293	kidney:	n/a	n/a
46	CTCF	chr2:58133364-58133568	GM10248	blood:	n/a	n/a
47	CTCF	chr2:58133400-58133550	GM06990	blood:	n/a	n/a
48	CTCF	chr2:58133380-58133530	GM12874	blood:	n/a	n/a
49	CTCF	chr2:58133383-58133526	MCF-7	breast:	n/a	n/a
50	CTCF	chr2:58133380-58133530	GM12866	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:58131028..58133565-chr2:58275828..58277987,2	MCF-7	breast:
2	chr2:58132702..58133921-chr2:58674913..58675821,15	MCF-7	breast:
3	chr2:58133383..58133906-chr2:58674883..58675813,3	K562	blood:
4	chr2:58133060..58135151-chr2:58272508..58275235,2	MCF-7	breast:
5	chr2:58133222..58134008-chr2:58674834..58675396,2	MCF-7	breast:

No data

Variant related genes	Relation type
VRK2	TF binding region
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10172295	0.82[CEU][hapmap]
rs1533725	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2030237	0.82[CEU][hapmap]
rs2312143	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465805	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678874	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2678895	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2678898	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2678902	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2678911	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678913	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678914	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678916	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678917	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678918	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2678919	0.93[ASN][1000 genomes]
rs2678920	0.93[ASN][1000 genomes]
rs2683632	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2716991	0.82[JPT][hapmap]
rs2717000	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2717005	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2717008	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2717025	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2717026	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2717028	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2717029	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2717030	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2717038	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2717039	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2717058	0.93[ASN][1000 genomes]
rs2717059	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2717060	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2717067	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6545669	0.81[YRI][hapmap]
rs6705924	0.86[YRI][hapmap]
rs6717480	0.83[CEU][hapmap]
rs6720288	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867740	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs951965	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010981	chr2:58013389-58205699	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv874199	chr2:58031249-58161520	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58132400-58135000	Enhancers	A549	lung
2	chr2:58133200-58134400	Enhancers	Brain Hippocampus Middle	brain
3	chr2:58133400-58133600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr2:58133400-58133800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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