Variant report

Variant	rs3753673
Chromosome Location	chr1:226129312-226129313
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	USF1	chr1:226129216-226129799	ECC-1	luminal epithelium:	n/a	chr1:226129551-226129572 chr1:226129556-226129565 chr1:226129557-226129566 chr1:226129557-226129566 chr1:226129555-226129568 chr1:226129558-226129567
2	USF1	chr1:226129311-226129731	A549	lung:	n/a	chr1:226129551-226129572 chr1:226129556-226129565 chr1:226129557-226129566 chr1:226129557-226129566 chr1:226129555-226129568 chr1:226129558-226129567
3	USF1	chr1:226129255-226129817	K562	blood:	n/a	chr1:226129551-226129572 chr1:226129556-226129565 chr1:226129557-226129566 chr1:226129557-226129566 chr1:226129555-226129568 chr1:226129558-226129567
4	USF1	chr1:226129278-226129720	H1-hESC	embryonic stem cell:	n/a	chr1:226129551-226129572 chr1:226129556-226129565 chr1:226129557-226129566 chr1:226129557-226129566 chr1:226129555-226129568 chr1:226129558-226129567
5	ZNF263	chr1:226129262-226129810	HEK293-T-REx	kidney:	n/a	n/a
6	USF1	chr1:226129223-226129863	K562	blood:	n/a	chr1:226129551-226129572 chr1:226129556-226129565 chr1:226129557-226129566 chr1:226129557-226129566 chr1:226129555-226129568 chr1:226129558-226129567
7	USF1	chr1:226129273-226129822	ECC-1	luminal epithelium:	n/a	chr1:226129551-226129572 chr1:226129556-226129565 chr1:226129557-226129566 chr1:226129557-226129566 chr1:226129555-226129568 chr1:226129558-226129567

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226110303..226113969-chr1:226129213..226132274,3	MCF-7	breast:
2	chr1:226096836..226099303-chr1:226126858..226129548,2	K562	blood:

Variant related genes	Relation type
ENSG00000248322	TF binding region
LEFTY2	TF binding region
ENSG00000143811	Chromatin interaction
ENSG00000243709	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10915902	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10915903	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28364597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3753675	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820237	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6426093	1.00[MEX][hapmap]
rs6661737	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	esv3385958	chr1:226117875-226149657	Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226126800-226129600	Enhancers	Placenta	Placenta
2	chr1:226126800-226129800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:226127000-226133000	Weak transcription	Gastric	stomach
4	chr1:226127200-226130600	Enhancers	Fetal Muscle Leg	muscle
5	chr1:226127200-226131200	Enhancers	Fetal Muscle Trunk	muscle
6	chr1:226127400-226131200	Enhancers	Fetal Heart	heart
7	chr1:226127400-226132200	Weak transcription	Fetal Thymus	thymus
8	chr1:226127600-226129600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:226127600-226130400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:226127600-226132200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:226127800-226129400	Enhancers	Brain Germinal Matrix	brain
12	chr1:226127800-226129600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:226127800-226129800	Enhancers	Ovary	ovary
14	chr1:226127800-226130600	Enhancers	Right Ventricle	heart
15	chr1:226127800-226130800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:226127800-226133000	Weak transcription	Pancreas	Pancrea
17	chr1:226128000-226129400	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:226128000-226129800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:226128000-226130000	Enhancers	Fetal Lung	lung
20	chr1:226128200-226129400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:226128200-226129800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:226128200-226129800	Enhancers	Lung	lung
23	chr1:226128200-226129800	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr1:226128200-226130000	Enhancers	Adipose Nuclei	Adipose
25	chr1:226128200-226130000	Enhancers	Left Ventricle	heart
26	chr1:226128200-226130600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:226128200-226130800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:226128200-226131000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:226128400-226129400	Enhancers	Stomach Smooth Muscle	stomach
30	chr1:226128400-226129600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:226128400-226129600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:226128400-226129800	Enhancers	Colonic Mucosa	Colon
33	chr1:226128600-226129600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:226128600-226129800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:226128600-226130000	Enhancers	Fetal Stomach	stomach
36	chr1:226128600-226130800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:226128600-226131800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr1:226128800-226129600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
39	chr1:226128800-226129600	Enhancers	Brain Cingulate Gyrus	brain
40	chr1:226128800-226129600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:226128800-226129800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:226128800-226130000	Enhancers	Spleen	Spleen
43	chr1:226128800-226130800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:226128800-226132600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:226129000-226129400	Weak transcription	Right Atrium	heart
46	chr1:226129000-226129600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:226129000-226129600	Enhancers	HepG2	liver
48	chr1:226129000-226129800	Enhancers	Esophagus	oesophagus
49	chr1:226129000-226130000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:226129200-226129400	Enhancers	Primary B cells from peripheral blood	blood

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