Variant report

Variant	rs12733799
Chromosome Location	chr1:186345497-186345498
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	POLR2A	chr1:186343484-186346756	MCF10A-Er-Src	breast:	n/a	n/a
2	CHD1	chr1:186344067-186345779	GM12878	blood:	n/a	chr1:186344825-186344835
3	TBP	chr1:186343433-186345520	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:186343407-186345626	K562	blood:	n/a	n/a
5	GABPA	chr1:186343774-186345649	MCF-7	breast:	n/a	chr1:186344824-186344833
6	POLR2A	chr1:186343447-186345545	K562	blood:	n/a	n/a
7	FOXA1	chr1:186345276-186345740	HepG2	liver:	n/a	n/a
8	MYC	chr1:186343499-186345841	K562	blood:	n/a	n/a
9	CUX1	chr1:186343439-186345835	K562	blood:	n/a	n/a
10	STAT3	chr1:186344403-186345649	GM12878	blood:	n/a	chr1:186344868-186344880 chr1:186344867-186344879
11	ARID3A	chr1:186344146-186345604	K562	blood:	n/a	n/a
12	ZNF143	chr1:186343908-186345517	K562	blood:	n/a	chr1:186344509-186344518 chr1:186344511-186344520 chr1:186344502-186344520
13	EP300	chr1:186344237-186345531	GM12878	blood:	n/a	n/a
14	IRF1	chr1:186344038-186345912	K562	blood:	n/a	chr1:186344937-186344946 chr1:186344823-186344837 chr1:186345429-186345441
15	POLR2A	chr1:186343981-186345575	K562	blood:	n/a	n/a
16	CREB1	chr1:186343914-186345884	K562	blood:	n/a	n/a
17	CHD1	chr1:186344658-186345662	H1-hESC	embryonic stem cell:	n/a	chr1:186344825-186344835
18	ARID3A	chr1:186344344-186345615	HepG2	liver:	n/a	n/a
19	REST	chr1:186343619-186345569	H1-neurons	neurons:	n/a	chr1:186345295-186345309
20	EP300	chr1:186343590-186345507	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:186343542-186345533	Hela-S3	cervix:	n/a	n/a
22	CREB1	chr1:186344075-186345521	H1-hESC	embryonic stem cell:	n/a	n/a
23	GTF2F1	chr1:186344245-186345616	K562	blood:	n/a	n/a
24	CHD2	chr1:186343449-186345548	Hela-S3	cervix:	n/a	chr1:186344825-186344835
25	POLR2A	chr1:186343445-186345514	GM12878	blood:	n/a	n/a
26	HCFC1	chr1:186343420-186345598	K562	blood:	n/a	n/a
27	KAP1	chr1:186343588-186345525	HEK293	kidney:	n/a	n/a
28	POLR2A	chr1:186343517-186345667	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:186343064-186345828	K562	blood:	n/a	n/a
30	E2F4	chr1:186344209-186345588	MCF10A-Er-Src	breast:	n/a	chr1:186344810-186344821 chr1:186344824-186344833 chr1:186344810-186344821
31	POLR2A	chr1:186343437-186345610	IMR90	lung:	n/a	n/a
32	RFX5	chr1:186343473-186345631	Hela-S3	cervix:	n/a	n/a
33	CREB1	chr1:186344035-186345506	GM12878	blood:	n/a	n/a
34	STAT5A	chr1:186344253-186345735	K562	blood:	n/a	chr1:186344868-186344880 chr1:186344867-186344879
35	KAP1	chr1:186345483-186346054	K562	blood:	n/a	n/a
36	POLR2A	chr1:186343380-186345527	MCF10A-Er-Src	breast:	n/a	n/a
37	ZMIZ1	chr1:186343592-186345617	K562	blood:	n/a	n/a
38	HCFC1	chr1:186342972-186346014	Hela-S3	cervix:	n/a	n/a
39	JUND	chr1:186344317-186345621	Hela-S3	cervix:	n/a	chr1:186344583-186344592
40	POLR2A	chr1:186343505-186345654	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:186279942..186281845-chr1:186343325..186346234,2	K562	blood:
2	chr1:186344996..186345598-chr5:94416998..94417779,2	Hela-S3	cervix:
3	chr1:186341227..186346056-chr1:193025925..193030298,4	K562	blood:
4	chr1:186345238..186346752-chr1:186365490..186368054,2	MCF-7	breast:
5	chr1:186345038..186345653-chr17:7387578..7388101,2	Hela-S3	cervix:
6	chr1:186312933..186317180-chr1:186341100..186346147,6	K562	blood:
7	chr1:186296941..186299348-chr1:186345485..186347021,2	K562	blood:
8	chr1:68150336..68151321-chr1:186344545..186345537,2	HCT-116	colon:
9	chr1:186345106..186345854-chr17:8150945..8151539,2	Hela-S3	cervix:

Variant related genes	Relation type
TPR	TF binding region
C1orf27	TF binding region
ENSG00000157181	Chromatin interaction
ENSG00000116717	Chromatin interaction
ENSG00000116750	Chromatin interaction
ENSG00000047410	Chromatin interaction
ENSG00000116747	Chromatin interaction
ENSG00000238754	Chromatin interaction
ENSG00000202025	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000175471	Chromatin interaction
ENSG00000268662	Chromatin interaction
ENSG00000178971	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11799811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11799843	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11801527	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs11803944	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap]
rs11805289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11805302	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11806068	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11806304	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[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11809402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11811320	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[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11812050	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12726960	0.82[CEU][hapmap]
rs12728791	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12739797	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12740221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12742751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12749203	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16825403	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1919194	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293569	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293570	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34467087	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34552348	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34924250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35131069	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35146131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35942197	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766698	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766701	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817586	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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57716405	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6682896	0.82[CHD][hapmap]
rs71634159	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv548399	chr1:186295930-186353461	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
4	esv1822818	chr1:186301447-186441585	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12733799	NCF2	cis	parietal	SCAN
rs12733799	TSEN15	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186342200-186346600	Active TSS	NHLF	lung
2	chr1:186342400-186345800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:186342400-186346000	Active TSS	Fetal Kidney	kidney
4	chr1:186342400-186346400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:186342600-186345800	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr1:186342600-186345800	Active TSS	NH-A	brain
7	chr1:186342600-186346000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:186342600-186346000	Active TSS	K562	blood
9	chr1:186342600-186346400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:186342600-186346400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:186342800-186345800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:186342800-186346000	Active TSS	Fetal Brain Female	brain
13	chr1:186342800-186346000	Active TSS	Fetal Stomach	stomach
14	chr1:186342800-186346000	Active TSS	HMEC	breast
15	chr1:186342800-186346000	Active TSS	NHDF-Ad	bronchial
16	chr1:186342800-186346200	Active TSS	A549	lung
17	chr1:186342800-186346400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:186342800-186349000	Active TSS	GM12878-XiMat	blood
19	chr1:186343000-186345800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:186343000-186345800	Active TSS	Fetal Intestine Large	intestine
21	chr1:186343000-186345800	Active TSS	Fetal Thymus	thymus
22	chr1:186343000-186345800	Active TSS	Hela-S3	cervix
23	chr1:186343000-186346000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:186343000-186346000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:186343000-186346000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:186343000-186346000	Active TSS	Fetal Muscle Leg	muscle
27	chr1:186343000-186346000	Active TSS	Psoas Muscle	Psoas
28	chr1:186343000-186346400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:186343200-186345600	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr1:186343200-186345600	Active TSS	Brain Hippocampus Middle	brain
31	chr1:186343200-186345600	Active TSS	Colon Smooth Muscle	Colon
32	chr1:186343200-186345600	Active TSS	Fetal Lung	lung
33	chr1:186343200-186345600	Active TSS	HUVEC	blood vessel
34	chr1:186343200-186345800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:186343200-186345800	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr1:186343200-186345800	Active TSS	Brain Anterior Caudate	brain
37	chr1:186343200-186345800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:186343200-186345800	Active TSS	Fetal Heart	heart
39	chr1:186343200-186345800	Active TSS	Fetal Intestine Small	intestine
40	chr1:186343200-186345800	Active TSS	Ovary	ovary
41	chr1:186343200-186345800	Active TSS	Placenta Amnion	Placenta Amnion
42	chr1:186343200-186345800	Active TSS	Thymus	Thymus
43	chr1:186343200-186346000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:186343200-186346000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:186343200-186346000	Active TSS	Right Ventricle	heart
46	chr1:186343200-186346000	Active TSS	HSMM	muscle
47	chr1:186343200-186346000	Active TSS	NHEK	skin
48	chr1:186343200-186346200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:186343200-186346400	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr1:186343200-186346400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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