Variant report

Variant	rs725299
Chromosome Location	chr1:95005105-95005106
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	chr1:95004816-95005515	Hela-S3	cervix:	n/a	n/a
2	FOS	chr1:95004708-95005855	MCF10A-Er-Src	breast:	n/a	chr1:95005291-95005301
3	CTCF	chr1:95005100-95005250	Hela-S3	cervix:	n/a	n/a
4	STAT3	chr1:95005074-95005435	MCF10A-Er-Src	breast:	n/a	chr1:95005149-95005156
5	PBX3	chr1:95004997-95005467	SK-N-SH	brain:	n/a	chr1:95005203-95005212
6	POLR2A	chr1:94992567-95005960	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
8	RAD21	chr1:95005043-95005922	IMR90	lung:	n/a	n/a
9	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
10	MXI1	chr1:95005093-95005576	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:95003836-95008278	U87	brain:	n/a	n/a
12	PBX3	chr1:95005050-95005467	SK-N-SH	brain:	n/a	chr1:95005203-95005212
13	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
14	POLR2A	chr1:95004799-95008370	Hela-S3	cervix:	n/a	n/a
15	RAD21	chr1:95005039-95005465	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:95004630-95008333	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:95005041-95005489	Hela-S3	cervix:	n/a	n/a
18	FOS	chr1:95004930-95005865	MCF10A-Er-Src	breast:	n/a	chr1:95005291-95005301
19	SMC3	chr1:95005015-95005828	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:95003842-95005922	U87	brain:	n/a	n/a
21	MAX	chr1:95005063-95008387	Hela-S3	cervix:	n/a	chr1:95006717-95006724 chr1:95006812-95006821
22	RFX5	chr1:95005068-95007782	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:94999692-95008368	ProgFib	skin:	n/a	n/a
24	TBP	chr1:95005043-95006937	Hela-S3	cervix:	n/a	n/a
25	MYC	chr1:95005070-95005526	MCF10A-Er-Src	breast:	n/a	n/a
26	MAZ	chr1:95004703-95008397	IMR90	lung:	n/a	chr1:95006717-95006724 chr1:95006812-95006821
27	MYC	chr1:95005072-95005419	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95004605..95005274-chr18:74502570..74503410,2	MCF-7	breast:
2	chr1:95004121..95007110-chr1:95017554..95021316,3	MCF-7	breast:

Variant related genes	Relation type
F3	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2021962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2021963	1.00[JPT][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3748017	1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs3917606	0.93[AMR][1000 genomes]
rs6692345	1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs698943	1.00[JPT][hapmap]
rs698944	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72968367	1.00[ASN][1000 genomes]
rs7531358	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs841698	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94965600-95006400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:94986000-95006200	Weak transcription	Liver	Liver
3	chr1:94994400-95005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:94994600-95005200	Weak transcription	Esophagus	oesophagus
5	chr1:94994600-95006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:94995200-95006200	Weak transcription	Spleen	Spleen
7	chr1:94996800-95005200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:94997600-95005200	Weak transcription	Gastric	stomach
9	chr1:94999000-95005400	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:95000400-95005600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
11	chr1:95001200-95006400	Weak transcription	Small Intestine	intestine
12	chr1:95001400-95006600	Transcr. at gene 5' and 3'	HMEC	breast
13	chr1:95001600-95006200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:95001600-95007400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:95001600-95007800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:95001800-95006000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:95001800-95006200	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:95001800-95007000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:95001800-95007800	Active TSS	Brain Hippocampus Middle	brain
20	chr1:95002000-95005400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:95002000-95006200	Weak transcription	Aorta	Aorta
22	chr1:95002200-95005200	Weak transcription	Fetal Muscle Leg	muscle
23	chr1:95002200-95006000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:95002400-95006600	Transcr. at gene 5' and 3'	NHLF	lung
25	chr1:95002600-95005800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:95002600-95006600	Active TSS	Fetal Brain Female	brain
27	chr1:95002800-95005400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:95002800-95005800	Enhancers	Fetal Brain Male	brain
29	chr1:95002800-95006800	Transcr. at gene 5' and 3'	NHEK	skin
30	chr1:95002800-95007200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:95002800-95007600	Active TSS	Brain Anterior Caudate	brain
32	chr1:95003000-95007800	Active TSS	Right Atrium	heart
33	chr1:95003000-95008400	Active TSS	Brain Angular Gyrus	brain
34	chr1:95003200-95006400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:95003200-95007800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:95003200-95007800	Active TSS	Fetal Intestine Large	intestine
37	chr1:95003400-95005200	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
38	chr1:95003400-95005200	Flanking Active TSS	Fetal Heart	heart
39	chr1:95003600-95005200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr1:95003800-95007600	Active TSS	Stomach Smooth Muscle	stomach
41	chr1:95003800-95007800	Active TSS	Brain Cingulate Gyrus	brain
42	chr1:95004000-95005200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
43	chr1:95004000-95005400	Active TSS	Colonic Mucosa	Colon
44	chr1:95004000-95005600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:95004000-95005800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
46	chr1:95004000-95006800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:95004200-95005800	Enhancers	HepG2	liver
48	chr1:95004200-95006000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:95004200-95006200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:95004200-95006800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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