Variant report

Variant	rs17002580
Chromosome Location	chr4:78274908-78274909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:69)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:69 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:78274880-78275030	MCF-7	breast:	n/a	n/a
2	CTCF	chr4:78274840-78274990	K562	blood:	n/a	n/a
3	CTCF	chr4:78274840-78274990	NHLF	lung:	n/a	n/a
4	CTCF	chr4:78274880-78275030	HFF-Myc	foreskin:	n/a	n/a
5	CTCF	chr4:78274860-78275010	GM12864	blood:	n/a	n/a
6	CTCF	chr4:78274860-78275010	BE2_C	brain:	n/a	n/a
7	CTCF	chr4:78274860-78275010	BJ	skin:	n/a	n/a
8	CTCF	chr4:78274860-78275010	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr4:78274840-78274990	HCM	heart:	n/a	n/a
10	CTCF	chr4:78274840-78274990	HMF	breast:	n/a	n/a
11	CTCF	chr4:78274840-78274990	A549	lung:	n/a	n/a
12	CTCF	chr4:78274840-78274990	RPTEC	kidney:	n/a	n/a
13	CTCF	chr4:78274820-78274970	AG04450	lung:	n/a	n/a
14	CTCF	chr4:78274860-78275010	GM12872	blood:	n/a	n/a
15	CTCF	chr4:78274860-78275010	GM12875	blood:	n/a	n/a
16	CTCF	chr4:78274860-78275010	GM12870	blood:	n/a	n/a
17	CTCF	chr4:78274870-78275069	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr4:78274880-78275030	WI-38	lung:	n/a	n/a
19	CTCF	chr4:78274860-78275010	HCPEpiC	choroid plexus:	n/a	n/a
20	CTCF	chr4:78274860-78275010	RPTEC	kidney:	n/a	n/a
21	CTCF	chr4:78274860-78275010	HVMF	connective:	n/a	n/a
22	CTCF	chr4:78274840-78274990	AG04450	lung:	n/a	n/a
23	CTCF	chr4:78274840-78274990	AG09319	gingival:	n/a	n/a
24	CTCF	chr4:78274800-78274950	SK-N-SH_RA	brain:	n/a	n/a
25	CTCF	chr4:78274840-78274990	GM12873	blood:	n/a	n/a
26	CTCF	chr4:78274860-78275010	HPAF	blood vessel:	n/a	n/a
27	CTCF	chr4:78274820-78274970	HPF	lung:	n/a	n/a
28	CTCF	chr4:78274840-78274990	HEEpiC	esophagus:	n/a	n/a
29	CTCF	chr4:78274860-78275010	HCT-116	colon:	n/a	n/a
30	CTCF	chr4:78274860-78275010	SAEC	small airway:	n/a	n/a
31	CTCF	chr4:78274860-78275010	AG09309	skin:	n/a	n/a
32	CTCF	chr4:78274840-78274990	NHDF-neo	bronchial:	n/a	n/a
33	CTCF	chr4:78274860-78275010	GM12878	blood:	n/a	n/a
34	CTCF	chr4:78274860-78275010	GM06990	blood:	n/a	n/a
35	CTCF	chr4:78274885-78275275	A549	lung:	n/a	chr4:78275103-78275121 chr4:78275105-78275126 chr4:78275106-78275119
36	CTCF	chr4:78274760-78274910	AG09319	gingival:	n/a	n/a
37	CTCF	chr4:78274840-78274990	GM12865	blood:	n/a	n/a
38	CTCF	chr4:78274860-78275010	HEK293	kidney:	n/a	n/a
39	CTCF	chr4:78274860-78275010	NHEK	skin:	n/a	n/a
40	CTCF	chr4:78274840-78274990	HMEC	breast:	n/a	n/a
41	CTCF	chr4:78274860-78275010	HMEC	breast:	n/a	n/a
42	CTCF	chr4:78274860-78275010	HEEpiC	esophagus:	n/a	n/a
43	CTCF	chr4:78274860-78275010	HAc	cerebellar:	n/a	n/a
44	CTCF	chr4:78274860-78275010	GM12868	blood:	n/a	n/a
45	CTCF	chr4:78274860-78275010	HepG2	liver:	n/a	n/a
46	CTCF	chr4:78274840-78274990	HCFaa	heart:	n/a	n/a
47	CTCF	chr4:78274860-78275010	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr4:78274840-78274990	AG10803	skin:	n/a	n/a
49	CTCF	chr4:78274860-78275010	HMF	breast:	n/a	n/a
50	CTCF	chr4:78274840-78274990	HCT-116	colon:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78270382..78272050-chr4:78274178..78276131,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000248831	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10016230	0.86[MEX][hapmap]
rs11930470	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11936421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12498728	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12499311	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12500776	0.93[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12501577	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12505837	0.81[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[AMR][1000 genomes]
rs12506515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12506585	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12511631	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1806738	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1806786	0.86[MEX][hapmap]
rs1962168	0.81[CEU][hapmap]
rs1962351	0.81[CEU][hapmap]
rs28477195	0.89[ASN][1000 genomes]
rs2903240	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4282207	0.86[MEX][hapmap]
rs4579145	0.86[MEX][hapmap]
rs67295944	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72648554	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72648563	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72648565	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72648566	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72648573	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72648578	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648580	0.83[ASN][1000 genomes]
rs72648581	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648583	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648584	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648585	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72648586	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72650413	0.87[AMR][1000 genomes]
rs7695467	0.81[CEU][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1002683	chr4:78170317-78281331	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1010450	chr4:78182037-78317840	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1004824	chr4:78188691-78312974	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1000447	chr4:78191608-78291173	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3468255	chr4:78237484-78277631	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv5935	chr4:78237568-78277734	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3468256	chr4:78237627-78277552	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1845782	chr4:78237955-78321598	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv829974	chr4:78240718-78415642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1000392	chr4:78273146-78301467	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1011607	chr4:78273146-78302096	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 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	chr4:78271800-78276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:78272000-78276800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:78272000-78277000	Weak transcription	HMEC	breast
4	chr4:78273800-78277000	Weak transcription	Fetal Heart	heart

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