Variant report

Variant	rs10072757
Chromosome Location	chr5:178946551-178946552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:178946453-178946609	MCF-7	breast:	n/a	chr5:178946578-178946587
2	CTCF	chr5:178946471-178946598	MCF-7	breast:	n/a	chr5:178946578-178946587
3	RAD21	chr5:178946532-178946679	GM12878	blood:	n/a	n/a
4	CTCF	chr5:178946450-178946675	K562	blood:	n/a	chr5:178946578-178946587
5	CTCF	chr5:178946491-178946619	GM12892	blood:	n/a	chr5:178946578-178946587
6	CTCF	chr5:178946506-178946661	GM10266	blood:	n/a	chr5:178946578-178946587
7	CTCF	chr5:178946486-178946654	Medullo	brain:	n/a	chr5:178946578-178946587
8	SMC3	chr5:178946522-178946670	HepG2	liver:	n/a	n/a
9	CTCF	chr5:178946541-178946650	GM13977	blood:	n/a	chr5:178946578-178946587
10	CTCF	chr5:178946540-178946690	HVMF	connective:	n/a	chr5:178946578-178946587
11	CTCF	chr5:178946455-178946688	LNCaP	prostate:	n/a	chr5:178946578-178946587
12	CTCF	chr5:178946493-178946639	GM19239	blood:	n/a	chr5:178946578-178946587
13	RCOR1	chr5:178946534-178946811	K562	blood:	n/a	n/a
14	RAD21	chr5:178946535-178946707	K562	blood:	n/a	n/a
15	RAD21	chr5:178946487-178946640	IMR90	lung:	n/a	n/a
16	CTCF	chr5:178946539-178946565	GM19240	blood:	n/a	n/a
17	FOXA1	chr5:178946531-178946721	T-47D	breast:	n/a	n/a
18	CTCF	chr5:178946471-178946665	HUVEC	blood vessel:	n/a	chr5:178946578-178946587
19	CTCF	chr5:178946453-178946678	A549	lung:	n/a	chr5:178946578-178946587
20	CTCF	chr5:178946547-178946591	A549	lung:	n/a	chr5:178946578-178946587
21	RAD21	chr5:178946472-178946650	HepG2	liver:	n/a	n/a
22	CTCF	chr5:178946465-178946658	K562	blood:	n/a	chr5:178946578-178946587
23	CTCF	chr5:178946471-178946606	MCF-7	breast:	n/a	chr5:178946578-178946587
24	CTCF	chr5:178946461-178946653	ProgFib	skin:	n/a	chr5:178946578-178946587
25	CTCF	chr5:178946494-178946650	GM10248	blood:	n/a	chr5:178946578-178946587
26	CTCF	chr5:178946463-178946693	K562	blood:	n/a	chr5:178946578-178946587
27	CTCF	chr5:178946480-178946641	GM13976	blood:	n/a	chr5:178946578-178946587
28	CTCF	chr5:178946500-178946650	GM12873	blood:	n/a	chr5:178946578-178946587
29	CTCF	chr5:178946460-178946669	Gliobla	brain:	n/a	chr5:178946578-178946587
30	CTCF	chr5:178946468-178946645	HepG2	liver:	n/a	chr5:178946578-178946587
31	CTCF	chr5:178946433-178946677	GM12878	blood:	n/a	chr5:178946578-178946587
32	CTCF	chr5:178946486-178946625	GM19238	blood:	n/a	chr5:178946578-178946587
33	CTCF	chr5:178946476-178946677	Pancreas_OC	pancreas:	n/a	chr5:178946578-178946587
34	GATA3	chr5:178946515-178946723	T-47D	breast:	n/a	n/a
35	SMC3	chr5:178946473-178946654	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr5:178946488-178946623	A549	lung:	n/a	chr5:178946578-178946587
37	CTCF	chr5:178946525-178946636	Kidney_OC	kidney:	n/a	chr5:178946578-178946587
38	CTCF	chr5:178946525-178946613	Fibrobl	skin:	n/a	chr5:178946578-178946587
39	CTCF	chr5:178946453-178946688	MCF-7	breast:	n/a	chr5:178946578-178946587
40	CTCF	chr5:178946479-178946647	IMR90	lung:	n/a	chr5:178946578-178946587
41	CTCF	chr5:178946463-178946708	LNCaP	prostate:	n/a	chr5:178946578-178946587
42	CTCF	chr5:178946424-178946705	MCF-7	breast:	n/a	chr5:178946578-178946587
43	CTCF	chr5:178946532-178946610	GM20000	blood:	n/a	chr5:178946578-178946587
44	CTCF	chr5:178946462-178946673	GM12878	blood:	n/a	chr5:178946578-178946587
45	FOXA1	chr5:178946521-178946800	T-47D	breast:	n/a	n/a
46	RAD21	chr5:178946451-178946651	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr5:178946520-178946670	Caco-2	colon:	n/a	chr5:178946578-178946587
48	CTCF	chr5:178946464-178946667	Hela-S3	cervix:	n/a	chr5:178946578-178946587
49	CTCF	chr5:178946471-178946693	Spleen_OC	spleen:	n/a	chr5:178946578-178946587
50	CTCF	chr5:178946426-178946757	K562	blood:	n/a	chr5:178946578-178946587

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178946216..178946980-chr5:179095346..179096018,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253652	TF binding region
ENSG00000251545	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10074573	0.80[CHD][hapmap]
rs4701130	0.80[CHD][hapmap]
rs4701131	0.80[CHD][hapmap]
rs4701132	0.80[CHD][hapmap]
rs6862387	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs6889447	0.80[CHB][hapmap]
rs7702303	0.80[CHD][hapmap]
rs7718673	0.80[CHD][hapmap]
rs7733389	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	esv2758031	chr5:178661266-179037529	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2759397	chr5:178661266-179037529	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv531996	chr5:178669297-178989687	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv34709	chr5:178720968-178961710	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	esv2757148	chr5:178720968-178961872	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3390865	chr5:178726226-178947989	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv34254	chr5:178749394-178961710	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv883260	chr5:178828854-178961710	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
11	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
12	nsv600658	chr5:178921861-178950814	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv883267	chr5:178925558-178951106	Weak transcription Enhancers 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
14	nsv883268	chr5:178928962-178951106	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv969932	chr5:178936510-178946894	Enhancers Weak transcription 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10072757	TRIM52	cis	cerebellum	SCAN
rs10072757	RUFY1	cis	parietal	SCAN
rs10072757	MGAT4B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178941000-178946800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:178943600-178946600	Weak transcription	HepG2	liver
3	chr5:178943600-178949000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:178946400-178946600	Enhancers	Fetal Brain Female	brain

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