Variant report

Variant	rs4304552
Chromosome Location	chr1:168543756-168543757
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:84)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:84 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:168543599-168543814	A549	lung:	n/a	n/a
2	CEBPB	chr1:168543469-168543784	A549	lung:	n/a	chr1:168543617-168543628
3	RAD21	chr1:168543573-168543840	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr1:168543579-168543846	Spleen_OC	spleen:	n/a	n/a
5	CTCF	chr1:168543608-168543813	NHEK	skin:	n/a	n/a
6	CTCF	chr1:168543359-168543854	SK-N-SH	brain:	n/a	n/a
7	RCOR1	chr1:168543635-168543766	K562	blood:	n/a	n/a
8	ZNF143	chr1:168543624-168543757	K562	blood:	n/a	n/a
9	CTCF	chr1:168543559-168543845	K562	blood:	n/a	n/a
10	CTCF	chr1:168543571-168543816	HepG2	liver:	n/a	n/a
11	RAD21	chr1:168543604-168543819	IMR90	lung:	n/a	n/a
12	CTCF	chr1:168543567-168543892	Medullo	brain:	n/a	n/a
13	SMC3	chr1:168543562-168543817	GM12878	blood:	n/a	n/a
14	CTCF	chr1:168543570-168543835	Gliobla	brain:	n/a	n/a
15	CEBPB	chr1:168543357-168543865	K562	blood:	n/a	chr1:168543617-168543628
16	RFX5	chr1:168543643-168543771	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr1:168543571-168543840	GM12878	blood:	n/a	n/a
18	CTCF	chr1:168543590-168543816	Fibrobl	skin:	n/a	n/a
19	RAD21	chr1:168543560-168543837	GM12878	blood:	n/a	n/a
20	TEAD4	chr1:168543508-168543856	H1-hESC	embryonic stem cell:	n/a	n/a
21	TEAD4	chr1:168543530-168543798	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr1:168543576-168543778	HepG2	liver:	n/a	n/a
23	TEAD4	chr1:168543474-168543805	K562	blood:	n/a	n/a
24	CTCF	chr1:168543573-168543843	MCF-7	breast:	n/a	n/a
25	GATA2	chr1:168543562-168543792	SH-SY5Y	brain:	n/a	n/a
26	SMC3	chr1:168543578-168543847	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr1:168543553-168543843	GM12878	blood:	n/a	n/a
28	CTCF	chr1:168543523-168543779	SK-N-SH_RA	brain:	n/a	n/a
29	CTCF	chr1:168543570-168543807	ECC-1	luminal epithelium:	n/a	n/a
30	CTCF	chr1:168543627-168543802	GM13977	blood:	n/a	n/a
31	CTCF	chr1:168543640-168543790	GM12865	blood:	n/a	n/a
32	CTCF	chr1:168543629-168543806	GM20000	blood:	n/a	n/a
33	CTCF	chr1:168543620-168543770	GM12866	blood:	n/a	n/a
34	CTCF	chr1:168543574-168543786	A549	lung:	n/a	n/a
35	RAD21	chr1:168543585-168543780	GM12878	blood:	n/a	n/a
36	RAD21	chr1:168543485-168543782	SK-N-SH_RA	brain:	n/a	n/a
37	CEBPD	chr1:168543461-168543805	K562	blood:	n/a	n/a
38	RAD21	chr1:168543439-168543804	HepG2	liver:	n/a	n/a
39	SMC3	chr1:168543577-168543847	K562	blood:	n/a	n/a
40	RAD21	chr1:168543502-168543814	H1-hESC	embryonic stem cell:	n/a	n/a
41	SMC3	chr1:168543384-168543852	SK-N-SH	brain:	n/a	n/a
42	CTCF	chr1:168543468-168543869	K562	blood:	n/a	n/a
43	CTCF	chr1:168543587-168543815	Kidney_OC	kidney:	n/a	n/a
44	RAD21	chr1:168543413-168543850	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr1:168543599-168543824	LNCaP	prostate:	n/a	n/a
46	CTCF	chr1:168543544-168543862	K562	blood:	n/a	n/a
47	RAD21	chr1:168543611-168543823	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr1:168543640-168543790	GM12864	blood:	n/a	n/a
49	CEBPB	chr1:168543459-168543808	K562	blood:	n/a	chr1:168543617-168543628
50	CTCF	chr1:168543588-168543808	GM10248	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168408738..168409696-chr1:168543083..168544145,4	MCF-7	breast:
2	chr1:168409048..168409630-chr1:168543648..168544296,2	K562	blood:

No data

Variant related genes	Relation type
XCL1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12029370	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12039757	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1933099	0.80[AMR][1000 genomes]
rs2143310	0.81[ASN][1000 genomes]
rs2143311	0.81[ASN][1000 genomes]
rs34038445	0.81[ASN][1000 genomes]
rs3753938	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4656155	0.81[ASN][1000 genomes]
rs470739	0.91[ASN][1000 genomes]
rs6700487	0.91[MEX][hapmap]
rs7354947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7532420	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014626	chr1:168441288-168642731	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535196	chr1:168441288-168642731	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1011821	chr1:168441488-168642592	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535197	chr1:168441488-168642592	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1008852	chr1:168449940-168643905	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv535198	chr1:168449940-168643905	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	esv1792733	chr1:168526394-168544716	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168539400-168550600	Weak transcription	HepG2	liver
2	chr1:168543400-168544200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:168543600-168545800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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