Variant report

Variant	rs61749312
Chromosome Location	chr3:49314128-49314129
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	POLR2A	chr3:49313891-49315337	GM12891	blood:	n/a	n/a
2	MAX	chr3:49313833-49314314	H1-hESC	embryonic stem cell:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
3	POU2F2	chr3:49313925-49314830	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:49313815-49315390	GM12892	blood:	n/a	n/a
5	CEBPB	chr3:49313957-49314613	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:49313870-49315078	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr3:49313706-49315442	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:49313935-49314902	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:49313982-49314214	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:49314091-49314926	SK-N-MC	brain:	n/a	n/a
11	RUNX3	chr3:49313789-49314834	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49314047-49315176	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:49314025-49314978	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr3:49314040-49314190	AG09319	gingival:	n/a	n/a
15	POLR2A	chr3:49314087-49315132	PBDE	blood:	n/a	n/a
16	RUNX3	chr3:49313793-49314908	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:49313785-49314858	U87	brain:	n/a	n/a
18	SMC3	chr3:49314107-49314298	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49314105-49314839	ECC-1	luminal epithelium:	n/a	n/a
20	NFATC1	chr3:49313836-49315065	GM12878	blood:	n/a	n/a
21	PML	chr3:49313557-49315281	GM12878	blood:	n/a	chr3:49315192-49315201
22	E2F6	chr3:49313720-49314926	H1-hESC	embryonic stem cell:	n/a	chr3:49314767-49314777
23	MAX	chr3:49313862-49314847	SK-N-SH	brain:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
24	FOXM1	chr3:49314126-49314820	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:49314024-49314892	GM19193	blood:	n/a	n/a
26	POLR2A	chr3:49313905-49314838	GM12878	blood:	n/a	n/a
27	CTCF	chr3:49314120-49314270	GM12873	blood:	n/a	n/a
28	MAX	chr3:49313749-49314907	ECC-1	luminal epithelium:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
29	WRNIP1	chr3:49313972-49314317	GM12878	blood:	n/a	n/a
30	MAX	chr3:49313881-49314175	NB4	blood:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
31	POLR2A	chr3:49313830-49314999	HL-60	blood:	n/a	n/a
32	MAX	chr3:49313810-49314255	H1-hESC	embryonic stem cell:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
33	TAF1	chr3:49313847-49314813	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr3:49313897-49314852	U87	brain:	n/a	n/a
35	POLR2A	chr3:49314105-49314239	K562	blood:	n/a	n/a
36	TCF12	chr3:49314112-49314905	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr3:49314115-49314863	GM12878	blood:	n/a	n/a
38	YY1	chr3:49314052-49314820	ECC-1	luminal epithelium:	n/a	chr3:49314463-49314471
39	BCL3	chr3:49313923-49314904	GM12878	blood:	n/a	chr3:49314526-49314539
40	BCLAF1	chr3:49313894-49314905	GM12878	blood:	n/a	chr3:49314526-49314539
41	POLR2A	chr3:49314057-49315161	PANC-1	pancreas:	n/a	n/a
42	YY1	chr3:49313835-49314491	H1-hESC	embryonic stem cell:	n/a	chr3:49314463-49314471
43	POLR2A	chr3:49314004-49314865	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAZ	chr3:49313736-49315010	IMR90	lung:	n/a	n/a
45	POLR2A	chr3:49313819-49315176	GM12891	blood:	n/a	n/a
46	POLR2A	chr3:49313762-49314985	GM12891	blood:	n/a	n/a
47	MAX	chr3:49313754-49314956	A549	lung:	n/a	chr3:49314049-49314059 chr3:49313988-49313998
48	CREB1	chr3:49313957-49314885	GM12878	blood:	n/a	n/a
49	BCLAF1	chr3:49313848-49314959	GM12878	blood:	n/a	chr3:49314526-49314539
50	MTA3	chr3:49313432-49315520	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49313590..49315716-chr3:49315985..49318300,2	MCF-7	breast:

Variant related genes	Relation type
C3orf62	TF binding region
ENSG00000114316	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11130201	0.86[AFR][1000 genomes]
rs11717485	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080567	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1996874	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55808753	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55990645	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56760510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58998762	1.00[EUR][1000 genomes]
rs59579780	0.83[AFR][1000 genomes]
rs60011446	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61008775	1.00[EUR][1000 genomes]
rs61744082	1.00[EUR][1000 genomes]
rs6446269	0.89[AFR][1000 genomes]
rs6446270	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.89[AFR][1000 genomes]
rs6446281	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[AMR][1000 genomes]
rs72934290	1.00[ASN][1000 genomes]
rs72934791	1.00[EUR][1000 genomes]
rs72936804	1.00[EUR][1000 genomes]
rs72936810	1.00[EUR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	1.00[EUR][1000 genomes]
rs73831435	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.83[AFR][1000 genomes]
rs73833525	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7646393	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.92[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833422	1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9877045	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv963481	chr3:49304260-49325571	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49301800-49315600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49303600-49315600	Weak transcription	HepG2	liver
3	chr3:49307200-49314200	Weak transcription	Hela-S3	cervix
4	chr3:49307400-49314600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:49307400-49314800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:49309200-49316000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:49311800-49315200	Weak transcription	K562	blood
8	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:49313200-49318600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:49313200-49326200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:49313200-49349400	Strong transcription	Dnd41	blood
12	chr3:49313400-49314200	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr3:49313400-49314400	Flanking Active TSS	Fetal Heart	heart
14	chr3:49313400-49314400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:49313400-49314400	Flanking Active TSS	GM12878-XiMat	blood
16	chr3:49313400-49318600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:49313600-49314200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:49313600-49314200	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr3:49313600-49314200	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr3:49313600-49314200	Flanking Active TSS	Rectal Smooth Muscle	rectum
21	chr3:49313600-49314200	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr3:49313600-49314400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:49313600-49314400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:49313600-49314400	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr3:49313600-49314400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr3:49313600-49314400	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr3:49313600-49314400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:49313600-49314400	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr3:49313600-49314400	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr3:49313600-49314400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr3:49313600-49314400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr3:49313600-49314400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:49313600-49314400	Flanking Active TSS	Fetal Intestine Small	intestine
34	chr3:49313600-49314400	Flanking Active TSS	Fetal Lung	lung
35	chr3:49313600-49314400	Flanking Active TSS	Fetal Stomach	stomach
36	chr3:49313600-49314400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr3:49313600-49314400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:49313600-49314400	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr3:49313600-49314400	Flanking Active TSS	NH-A	brain
40	chr3:49313600-49314400	Flanking Active TSS	Osteobl	bone
41	chr3:49313600-49314800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr3:49313600-49315000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:49313600-49315000	Active TSS	Aorta	Aorta
44	chr3:49313600-49315000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr3:49313600-49315200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:49313600-49315200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:49313600-49315200	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr3:49313600-49315200	Transcr. at gene 5' and 3'	Placenta	Placenta
49	chr3:49313600-49315200	Flanking Active TSS	HUVEC	blood vessel
50	chr3:49313600-49315200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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