Variant report

Variant	rs11562954
Chromosome Location	chr2:234837513-234837514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:117)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:117 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:234837341-234837526	GM12891	blood:	n/a	n/a
2	RAD21	chr2:234837192-234837603	A549	lung:	n/a	n/a
3	RAD21	chr2:234837345-234837530	K562	blood:	n/a	n/a
4	CTCF	chr2:234837420-234837570	NHDF-neo	bronchial:	n/a	n/a
5	CTCF	chr2:234837130-234837768	HCT-116	colon:	n/a	n/a
6	CTCF	chr2:234837336-234837557	LNCaP	prostate:	n/a	n/a
7	CTCF	chr2:234837380-234837530	AG04449	skin:	n/a	n/a
8	RAD21	chr2:234837207-234837543	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr2:234837329-234837552	MCF-7	breast:	n/a	n/a
10	CTCF	chr2:234837328-234837548	MCF-7	breast:	n/a	n/a
11	CTCF	chr2:234837380-234837530	NHLF	lung:	n/a	n/a
12	CTCF	chr2:234837250-234837630	IMR90	lung:	n/a	n/a
13	CTCF	chr2:234837359-234837531	GM13977	blood:	n/a	n/a
14	CTCF	chr2:234837380-234837530	WERI-Rb-1	eye:	n/a	n/a
15	CTCF	chr2:234837300-234837550	GM12868	blood:	n/a	n/a
16	CTCF	chr2:234837420-234837570	GM12874	blood:	n/a	n/a
17	CTCF	chr2:234837290-234837532	A549	lung:	n/a	n/a
18	RAD21	chr2:234837323-234837531	K562	blood:	n/a	n/a
19	CTCF	chr2:234837311-234837545	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr2:234837349-234837533	ProgFib	skin:	n/a	n/a
21	CTCF	chr2:234837380-234837530	GM12875	blood:	n/a	n/a
22	CTCF	chr2:234837420-234837570	NHEK	skin:	n/a	n/a
23	CTCF	chr2:234837348-234837547	A549	lung:	n/a	n/a
24	CTCF	chr2:234837259-234837614	GM12878	blood:	n/a	n/a
25	ZNF143	chr2:234837304-234837567	GM12878	blood:	n/a	n/a
26	CTCF	chr2:234837189-234837609	A549	lung:	n/a	n/a
27	CTCF	chr2:234837400-234837550	HEEpiC	esophagus:	n/a	n/a
28	CTCF	chr2:234837312-234837563	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr2:234837343-234837532	GM12892	blood:	n/a	n/a
30	CTCF	chr2:234837380-234837530	BE2_C	brain:	n/a	n/a
31	RAD21	chr2:234837167-234837679	ECC-1	luminal epithelium:	n/a	n/a
32	CTCF	chr2:234837440-234837590	HEK293	kidney:	n/a	n/a
33	RAD21	chr2:234837223-234837550	SK-N-SH_RA	brain:	n/a	n/a
34	SMC3	chr2:234837118-234838146	SK-N-SH	brain:	n/a	n/a
35	RAD21	chr2:234837319-234837569	GM12878	blood:	n/a	n/a
36	CTCF	chr2:234837420-234837570	AG04450	lung:	n/a	n/a
37	CTCF	chr2:234837440-234837590	A549	lung:	n/a	n/a
38	CTCF	chr2:234837333-234837556	K562	blood:	n/a	n/a
39	CTCF	chr2:234837400-234837550	BE2_C	brain:	n/a	n/a
40	CTCF	chr2:234837352-234837523	Fibrobl	skin:	n/a	n/a
41	CTCF	chr2:234837189-234837588	MCF-7	breast:	n/a	n/a
42	CTCF	chr2:234837158-234837672	HCT-116	colon:	n/a	n/a
43	CTCF	chr2:234837020-234837860	A549	lung:	n/a	n/a
44	RAD21	chr2:234837125-234837682	A549	lung:	n/a	n/a
45	CTCF	chr2:234837380-234837530	HL-60	blood:	n/a	n/a
46	CTCF	chr2:234837380-234837530	GM12865	blood:	n/a	n/a
47	CTCF	chr2:234837356-234837532	Spleen_OC	spleen:	n/a	n/a
48	CTCF	chr2:234837333-234837548	Gliobla	brain:	n/a	n/a
49	CTCF	chr2:234837440-234837590	HCM	heart:	n/a	n/a
50	RAD21	chr2:234837274-234837601	IMR90	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234357015..234358200-chr2:234837198..234838061,3	MCF-7	breast:
2	chr2:234835606..234837772-chr2:234955390..234957030,2	K562	blood:
3	chr2:234357304..234357929-chr2:234836996..234837769,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRPM8	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1004478	0.93[CEU][hapmap]
rs10490010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803665	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10803666	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470426	0.85[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12473889	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13028228	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17862920	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs17862921	0.93[CEU][hapmap];0.89[TSI][hapmap]
rs17863838	0.93[CEU][hapmap]
rs17863841	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17863842	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17864741	0.93[CEU][hapmap]
rs17868384	0.89[EUR][1000 genomes]
rs6741751	0.93[CEU][hapmap]
rs67646620	0.89[EUR][1000 genomes]
rs7558436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7562952	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs7562971	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7577262	0.93[CEU][hapmap];0.88[TSI][hapmap]
rs9646718	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11562954	APOBEC3B	trans	cerebellum	SCAN
rs11562954	NMUR1	cis	parietal	SCAN
rs11562954	COL6A3	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234834400-234838000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234836200-234838000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:234836200-234838000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:234837000-234838400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:234837000-234838600	Enhancers	A549	lung
6	chr2:234837200-234838000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:234837400-234839000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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