Variant report

Variant	rs12040650
Chromosome Location	chr1:184986725-184986726
allele	C/T
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	FOSL2	chr1:184986293-184986992	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:184986423-184986809	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr1:184986399-184986804	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:184986484-184986844	MCF-7	breast:	n/a	chr1:184986640-184986651
5	FOS	chr1:184986392-184986875	MCF10A-Er-Src	breast:	n/a	chr1:184986587-184986598
6	JUND	chr1:184986445-184986772	HepG2	liver:	n/a	chr1:184986587-184986598
7	CEBPB	chr1:184986149-184986856	Hela-S3	cervix:	n/a	chr1:184986640-184986651
8	STAT3	chr1:184986409-184986805	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr1:184986122-184986992	HCT-116	colon:	n/a	chr1:184986587-184986598
10	CEBPB	chr1:184986138-184987104	HCT-116	colon:	n/a	chr1:184986640-184986651
11	FOSL1	chr1:184986137-184987159	HCT-116	colon:	n/a	n/a
12	FOSL2	chr1:184986421-184986831	SK-N-SH	brain:	n/a	n/a
13	JUN	chr1:184986420-184986777	Hela-S3	cervix:	n/a	n/a
14	CEBPB	chr1:184986465-184986837	K562	blood:	n/a	chr1:184986640-184986651
15	FOS	chr1:184986440-184986796	Hela-S3	cervix:	n/a	chr1:184986587-184986598
16	JUND	chr1:184986165-184987328	SK-N-SH	brain:	n/a	chr1:184986587-184986598
17	CEBPB	chr1:184986436-184986851	IMR90	lung:	n/a	chr1:184986640-184986651
18	JUN	chr1:184985702-184987064	K562	blood:	n/a	n/a
19	FOSL2	chr1:184986393-184986797	MCF-7	breast:	n/a	n/a
20	JUND	chr1:184986275-184986920	SK-N-SH	brain:	n/a	chr1:184986587-184986598
21	FOS	chr1:184986401-184986812	MCF10A-Er-Src	breast:	n/a	chr1:184986587-184986598
22	JUND	chr1:184986227-184986805	Hela-S3	cervix:	n/a	chr1:184986587-184986598
23	FOSL2	chr1:184986443-184986805	A549	lung:	n/a	n/a
24	JUND	chr1:184986072-184986992	HCT-116	colon:	n/a	chr1:184986587-184986598
25	JUND	chr1:184985974-184986892	K562	blood:	n/a	chr1:184986587-184986598
26	CEBPB	chr1:184986485-184986727	K562	blood:	n/a	chr1:184986640-184986651
27	CEBPB	chr1:184986357-184986983	A549	lung:	n/a	chr1:184986640-184986651
28	STAT3	chr1:184986389-184986831	MCF10A-Er-Src	breast:	n/a	n/a
29	FOSL2	chr1:184986278-184986906	A549	lung:	n/a	n/a
30	FOS	chr1:184986370-184986789	HUVEC	blood vessel:	n/a	chr1:184986587-184986598
31	CEBPB	chr1:184986562-184986815	HepG2	liver:	n/a	chr1:184986640-184986651
32	CEBPB	chr1:184986525-184986782	ECC-1	luminal epithelium:	n/a	chr1:184986640-184986651
33	CEBPB	chr1:184986482-184986824	K562	blood:	n/a	chr1:184986640-184986651
34	ATF1	chr1:184986573-184986850	K562	blood:	n/a	n/a
35	MYC	chr1:184986517-184986805	MCF10A-Er-Src	breast:	n/a	n/a
36	SP1	chr1:184985961-184986987	HCT-116	colon:	n/a	n/a
37	MAFF	chr1:184986447-184986898	K562	blood:	n/a	n/a
38	FOSL1	chr1:184986216-184987025	HCT-116	colon:	n/a	n/a
39	ESR1	chr1:184986606-184986912	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:184986365-184986789	HCT-116	colon:	n/a	n/a
41	FOS	chr1:184986321-184986848	MCF10A-Er-Src	breast:	n/a	chr1:184986587-184986598
42	JUND	chr1:184986329-184986907	SK-N-SH	brain:	n/a	chr1:184986587-184986598
43	TCF12	chr1:184986225-184986928	SK-N-SH	brain:	n/a	n/a
44	CEBPB	chr1:184986466-184986815	A549	lung:	n/a	chr1:184986640-184986651
45	MAFK	chr1:184986202-184986975	K562	blood:	n/a	n/a
46	FOS	chr1:184986396-184986812	MCF10A-Er-Src	breast:	n/a	chr1:184986587-184986598
47	TEAD4	chr1:184986453-184986824	K562	blood:	n/a	n/a
48	KAP1	chr1:184986162-184986910	U2OS	brain:	n/a	n/a
49	CEBPB	chr1:184986426-184986894	MCF-7	breast:	n/a	chr1:184986640-184986651
50	SP1	chr1:184985970-184987064	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:184985716..184988331-chr1:184988994..184992281,3	K562	blood:
2	chr1:184948681..184951312-chr1:184986477..184988243,2	K562	blood:
3	chr1:184986624..184988154-chr1:185012581..185015445,2	K562	blood:
4	chr1:184984889..184988154-chr1:185012581..185015445,4	K562	blood:

Variant related genes	Relation type
RNA5SP72	TF binding region
ENSG00000121481	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1008502	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1046592	1.00[CEU][hapmap]
rs10489581	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap]
rs10797997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10797998	1.00[CEU][hapmap]
rs10911674	1.00[ASW][hapmap]
rs10911686	0.91[AMR][1000 genomes]
rs12022419	1.00[ASW][hapmap];0.85[TSI][hapmap]
rs12023744	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12027607	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12028809	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs12035073	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12037692	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12038919	1.00[ASW][hapmap]
rs12043427	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12043495	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12043617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12044161	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12049293	0.80[EUR][1000 genomes]
rs12064938	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12086086	1.00[CEU][hapmap]
rs12094983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12401293	0.86[AMR][1000 genomes]
rs12404644	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs12408279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs12408500	0.86[AMR][1000 genomes]
rs12409926	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1407554	1.00[CEU][hapmap]
rs1544052	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs16823740	0.92[EUR][1000 genomes]
rs2378958	1.00[ASW][hapmap]
rs3766720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs3766723	1.00[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs3806243	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes]
rs72724103	0.91[AMR][1000 genomes]
rs72724108	0.82[AMR][1000 genomes]
rs72739677	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72739679	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72741816	0.86[AMR][1000 genomes]
rs72741817	0.87[AMR][1000 genomes]
rs72741819	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv525731	chr1:184812165-185038104	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv872585	chr1:184813885-184986725	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv872587	chr1:184820832-184986725	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv522073	chr1:184986725-185013349	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184984000-184987600	Enhancers	Fetal Intestine Large	intestine
2	chr1:184984600-184987400	Enhancers	K562	blood
3	chr1:184985000-184987200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:184985600-184987000	Enhancers	Hela-S3	cervix
5	chr1:184985600-184987400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:184985800-184987000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:184985800-184987000	Enhancers	Osteobl	bone
8	chr1:184985800-184987400	Enhancers	HMEC	breast
9	chr1:184985800-184987400	Enhancers	NHDF-Ad	bronchial
10	chr1:184985800-184987600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:184986000-184986800	Enhancers	NHLF	lung
12	chr1:184986000-184987000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:184986000-184987000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:184986000-184987000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:184986000-184987000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:184986000-184987000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr1:184986000-184987000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:184986000-184987000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:184986000-184987000	Enhancers	NHEK	skin
20	chr1:184986000-184987200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:184986000-184987200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:184986200-184987000	Enhancers	NH-A	brain
23	chr1:184986200-184987400	Enhancers	HSMM	muscle
24	chr1:184986400-184986800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:184986600-184987200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:184986600-184987200	Enhancers	A549	lung

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