Variant report

Variant	rs3806440
Chromosome Location	chr1:113249555-113249556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:157)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:157 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:113249424-113250316	K562	blood:	n/a	n/a
2	POLR2A	chr1:113249301-113250183	HEK293	kidney:	n/a	n/a
3	RAD21	chr1:113249462-113250487	HCT-116	colon:	n/a	chr1:113250089-113250108 chr1:113250225-113250234
4	POLR2A	chr1:113249413-113250186	PFSK-1	brain:	n/a	n/a
5	BRCA1	chr1:113249383-113249564	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:113249187-113249722	HepG2	liver:	n/a	n/a
7	HEY1	chr1:113249461-113250061	K562	blood:	n/a	n/a
8	POLR2A	chr1:113249548-113249752	GM12891	blood:	n/a	n/a
9	ZBTB7A	chr1:113249152-113250338	K562	blood:	n/a	chr1:113249486-113249494 chr1:113249525-113249536
10	POLR2A	chr1:113249511-113250101	GM15510	blood:	n/a	n/a
11	SIN3AK20	chr1:113249442-113250302	K562	blood:	n/a	n/a
12	POLR2A	chr1:113249504-113250059	MCF-7	breast:	n/a	n/a
13	MXI1	chr1:113249306-113250399	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:113249448-113250318	HCT-116	colon:	n/a	n/a
15	POLR2A	chr1:113249505-113250110	GM18505	blood:	n/a	n/a
16	POLR2A	chr1:113249481-113250463	HCT-116	colon:	n/a	n/a
17	POLR2A	chr1:113249363-113250172	K562	blood:	n/a	n/a
18	SIN3A	chr1:113248991-113250599	H1-hESC	embryonic stem cell:	n/a	chr1:113249533-113249544
19	POLR2A	chr1:113249495-113250222	GM18951	blood:	n/a	n/a
20	SIN3AK20	chr1:113249530-113250186	K562	blood:	n/a	n/a
21	MAX	chr1:113249521-113250339	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:113249410-113250019	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:113249421-113250555	Hela-S3	cervix:	n/a	n/a
24	MAX	chr1:113249548-113250257	K562	blood:	n/a	n/a
25	POLR2A	chr1:113248962-113250483	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr1:113249476-113250541	Hela-S3	cervix:	n/a	n/a
27	MAZ	chr1:113246923-113250658	IMR90	lung:	n/a	chr1:113247387-113247397 chr1:113248122-113248131
28	CREB1	chr1:113249495-113250217	A549	lung:	n/a	n/a
29	ZBTB7A	chr1:113249027-113250567	ECC-1	luminal epithelium:	n/a	chr1:113249486-113249494 chr1:113249525-113249536
30	TAF1	chr1:113249515-113250239	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:113249392-113250044	GM12878	blood:	n/a	n/a
32	ZKSCAN1	chr1:113249519-113249661	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr1:113249549-113250190	GM12878	blood:	n/a	n/a
34	CHD1	chr1:113249418-113249764	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:113249494-113249772	HepG2	liver:	n/a	n/a
36	EGR1	chr1:113249550-113250167	K562	blood:	n/a	chr1:113249887-113249897 chr1:113249805-113249819
37	PAX5	chr1:113249466-113249831	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:113247261-113250309	HUVEC	blood vessel:	n/a	n/a
39	TAF1	chr1:113249491-113250031	K562	blood:	n/a	n/a
40	POLR2A	chr1:113249114-113250302	U87	brain:	n/a	n/a
41	SMC3	chr1:113249100-113250671	SK-N-SH	brain:	n/a	chr1:113250093-113250107
42	POLR2A	chr1:113249445-113250174	GM19099	blood:	n/a	n/a
43	POLR2A	chr1:113249068-113250356	K562	blood:	n/a	n/a
44	POLR2A	chr1:113249516-113250022	NB4	blood:	n/a	n/a
45	PAX5	chr1:113249503-113249803	GM12878	blood:	n/a	n/a
46	TCF3	chr1:113249464-113250296	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:113249463-113250115	U87	brain:	n/a	n/a
48	HMGN3	chr1:113249185-113250260	K562	blood:	n/a	n/a
49	POLR2A	chr1:113249492-113250471	Hela-S3	cervix:	n/a	n/a
50	GABPA	chr1:113249504-113249832	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113248698..113251078-chr1:113932422..113935147,2	MCF-7	breast:
3	chr1:113160723..113165170-chr1:113245654..113250392,12	K562	blood:
4	chr1:113246571..113250786-chr1:113261233..113263716,3	K562	blood:
5	chr1:112938761..112941761-chr1:113247568..113249753,3	MCF-7	breast:
6	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
7	chr1:113156399..113165396-chr1:113241191..113253782,55	MCF-7	breast:
8	chr1:113214590..113222957-chr1:113244863..113253590,39	MCF-7	breast:
9	chr1:113216859..113217827-chr1:113249275..113250031,2	MCF-7	breast:
10	chr1:113160834..113162243-chr1:113249295..113250445,3	MCF-7	breast:
11	chr1:113167976..113172227-chr1:113246480..113250465,5	K562	blood:
12	chr1:112933576..112940137-chr1:113246857..113251993,14	MCF-7	breast:
13	chr1:113008643..113012570-chr1:113247176..113250622,4	MCF-7	breast:
14	chr1:113193696..113198407-chr1:113243250..113250056,8	K562	blood:
15	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:
16	chr1:113156746..113166477-chr1:113240630..113253423,46	MCF-7	breast:

No data

Variant related genes	Relation type
RHOC	TF binding region
ENSG00000143079	Chromatin interaction
ENSG00000238975	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000134245	Chromatin interaction
ENSG00000184599	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	esv3358595	chr1:113248454-113251002	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113246800-113249600	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr1:113246800-113249600	Flanking Active TSS	Dnd41	blood
3	chr1:113247000-113249600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:113247200-113250400	Active TSS	Aorta	Aorta
5	chr1:113247400-113249600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr1:113247400-113250200	Active TSS	Psoas Muscle	Psoas
7	chr1:113247400-113250400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:113247400-113250400	Active TSS	Ovary	ovary
9	chr1:113247400-113250400	Active TSS	Right Atrium	heart
10	chr1:113247400-113250400	Active TSS	A549	lung
11	chr1:113247600-113249600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
12	chr1:113247600-113250200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:113247600-113250400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:113247600-113250400	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr1:113247600-113250600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:113247800-113250000	Flanking Active TSS	Primary hematopoietic stem cells	blood
17	chr1:113248000-113250200	Active TSS	Placenta Amnion	Placenta Amnion
18	chr1:113248000-113250200	Active TSS	NHLF	lung
19	chr1:113248000-113250400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:113248200-113250600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:113248400-113249600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:113248400-113250200	Active TSS	Fetal Kidney	kidney
23	chr1:113248600-113250000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:113248600-113250000	Active TSS	HMEC	breast
25	chr1:113248600-113250200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:113248600-113250200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:113248600-113250200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:113248600-113250200	Active TSS	Brain Anterior Caudate	brain
29	chr1:113248600-113250200	Active TSS	Lung	lung
30	chr1:113248600-113250200	Active TSS	HSMM	muscle
31	chr1:113248600-113250200	Active TSS	NHDF-Ad	bronchial
32	chr1:113248600-113250400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:113248600-113250400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:113248800-113249600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:113248800-113249600	Active TSS	Stomach Mucosa	stomach
36	chr1:113248800-113250000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:113248800-113250000	Active TSS	Gastric	stomach
38	chr1:113248800-113250000	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:113248800-113250200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:113248800-113250200	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr1:113248800-113250200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:113248800-113250200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr1:113248800-113250200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:113248800-113250200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:113248800-113250200	Active TSS	Muscle Satellite Cultured Cells	--
46	chr1:113248800-113250200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:113248800-113250200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:113248800-113250200	Active TSS	Brain Substantia Nigra	brain
49	chr1:113248800-113250200	Active TSS	Fetal Intestine Small	intestine
50	chr1:113248800-113250200	Active TSS	Fetal Stomach	stomach

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