Variant report

Variant	rs549386409
Chromosome Location	chr1:47081723-47081724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:47081533-47083316	K562	blood:	n/a	n/a
2	POLR2A	chr1:47081652-47082834	K562	blood:	n/a	n/a
3	RCOR1	chr1:47080951-47083959	IMR90	lung:	n/a	n/a
4	POLR2A	chr1:47081453-47083127	Hela-S3	cervix:	n/a	n/a
5	SMARCB1	chr1:47081719-47082955	Hela-S3	cervix:	n/a	n/a
6	ELK1	chr1:47081418-47082916	GM12878	blood:	n/a	n/a
7	ELF1	chr1:47081404-47082893	GM12878	blood:	n/a	n/a
8	EGR1	chr1:47081711-47082338	ECC-1	luminal epithelium:	n/a	chr1:47082045-47082059 chr1:47082049-47082058 chr1:47082049-47082060
9	POLR2A	chr1:47081085-47082992	GM12891	blood:	n/a	n/a
10	CHD2	chr1:47081354-47082855	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr1:47081487-47082958	GM12878	blood:	n/a	n/a
12	TEAD4	chr1:47081583-47082540	K562	blood:	n/a	n/a
13	PML	chr1:47081709-47082796	GM12878	blood:	n/a	n/a
14	CHD2	chr1:47081678-47081985	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:47081083-47082978	GM12878	blood:	n/a	n/a
16	WRNIP1	chr1:47081432-47083222	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:47081620-47081799	GM12878	blood:	n/a	n/a
18	MAZ	chr1:47081502-47083027	GM12878	blood:	n/a	n/a
19	RUNX3	chr1:47081318-47082746	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:47081012-47082875	GM19193	blood:	n/a	n/a
21	POLR2A	chr1:47081258-47082998	GM12878	blood:	n/a	n/a
22	SMARCC1	chr1:47081534-47083403	Hela-S3	cervix:	n/a	n/a
23	RFX5	chr1:47081714-47082719	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:47081376-47082947	GM18951	blood:	n/a	n/a
25	POLR2A	chr1:47081283-47081965	GM12878	blood:	n/a	n/a
26	E2F6	chr1:47081630-47083195	K562	blood:	n/a	chr1:47082336-47082345
27	RUNX3	chr1:47081344-47082621	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:47081395-47082943	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:47081355-47082879	GM15510	blood:	n/a	n/a
30	MAFK	chr1:47081561-47081760	K562	blood:	n/a	n/a
31	POLR2A	chr1:47081384-47083061	GM12878	blood:	n/a	n/a
32	MTA3	chr1:47081339-47083135	GM12878	blood:	n/a	n/a
33	MXI1	chr1:47081514-47082986	GM12878	blood:	n/a	n/a
34	POLR2A	chr1:47081720-47082838	Hela-S3	cervix:	n/a	n/a
35	MAX	chr1:47081491-47082940	GM12878	blood:	n/a	n/a
36	MAZ	chr1:47080667-47083935	IMR90	lung:	n/a	chr1:47083058-47083068
37	POLR2A	chr1:47081243-47083109	GM18505	blood:	n/a	n/a
38	POLR2A	chr1:47081133-47081802	GM12892	blood:	n/a	n/a
39	MAZ	chr1:47081486-47083313	K562	blood:	n/a	chr1:47083058-47083068
40	MXI1	chr1:47081458-47083082	IMR90	lung:	n/a	n/a
41	POLR2A	chr1:47081394-47082950	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47079661..47082285-chr1:47135813..47137705,2	K562	blood:
2	chr1:47069390..47072755-chr1:47079314..47082367,4	MCF-7	breast:
3	chr1:47080354..47082092-chr1:47110886..47112430,2	MCF-7	breast:
4	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
5	chr1:47080724..47082396-chr1:47183672..47185631,2	MCF-7	breast:
6	chr1:47077660..47081751-chr1:47132686..47135354,3	MCF-7	breast:
7	chr1:47078421..47080865-chr1:47080975..47083544,2	MCF-7	breast:

No data

Variant related genes	Relation type
MOB3C	TF binding region
ENSG00000186118	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000142961	Chromatin interaction
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription 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 miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv522319	chr1:47080741-47094267	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47076800-47081800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr1:47077000-47082000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:47078800-47081800	Enhancers	Spleen	Spleen
4	chr1:47079000-47082000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr1:47079000-47082000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:47079200-47081800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:47079400-47081800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr1:47079800-47081800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:47080200-47082000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:47080200-47082200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:47080400-47082000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:47080600-47082400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:47080800-47081800	Enhancers	Small Intestine	intestine
14	chr1:47080800-47081800	Flanking Active TSS	GM12878-XiMat	blood
15	chr1:47080800-47082000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:47080800-47082000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:47080800-47082000	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr1:47080800-47082000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:47080800-47082000	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr1:47081000-47081800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:47081000-47081800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:47081000-47081800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:47081000-47081800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:47081000-47081800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:47081000-47081800	Flanking Active TSS	Pancreas	Pancrea
26	chr1:47081000-47081800	Flanking Active TSS	NHLF	lung
27	chr1:47081000-47082000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:47081000-47082000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:47081000-47082000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr1:47081000-47082000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr1:47081000-47082000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr1:47081000-47082000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:47081000-47082000	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr1:47081000-47082000	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr1:47081000-47082000	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr1:47081000-47082000	Flanking Active TSS	Placenta	Placenta
37	chr1:47081000-47082000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr1:47081000-47082000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:47081000-47082000	Flanking Active TSS	Hela-S3	cervix
40	chr1:47081000-47082000	Flanking Active TSS	NHEK	skin
41	chr1:47081000-47082200	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr1:47081000-47082200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:47081200-47081800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:47081200-47081800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr1:47081200-47081800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr1:47081200-47081800	Flanking Active TSS	Right Atrium	heart
47	chr1:47081200-47081800	Flanking Active TSS	HMEC	breast
48	chr1:47081200-47081800	Flanking Active TSS	HSMM	muscle
49	chr1:47081200-47081800	Flanking Active TSS	HSMMtube	muscle
50	chr1:47081200-47082000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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