Variant report

Variant	rs2609401
Chromosome Location	chr1:223100163-223100164
allele	C/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	chr1:223100096-223100293	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:223100115-223100201	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:223100039-223100329	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr1:223099835-223100468	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:223099861-223100417	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr1:223100040-223100190	RPTEC	kidney:	n/a	n/a
7	CTCF	chr1:223100120-223100270	SAEC	small airway:	n/a	n/a
8	STAT3	chr1:223100090-223100264	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr1:223099937-223100425	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr1:223100089-223100263	MCF10A-Er-Src	breast:	n/a	n/a
11	RAD21	chr1:223099985-223100342	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAFK	chr1:223099837-223100276	IMR90	lung:	n/a	chr1:223099952-223099967
13	CTCF	chr1:223100140-223100290	HA-sp	spinal cord:	n/a	n/a
14	STAT3	chr1:223100078-223100322	MCF10A-Er-Src	breast:	n/a	n/a
15	RAD21	chr1:223100110-223100369	H1-hESC	embryonic stem cell:	n/a	n/a
16	MYC	chr1:223099975-223100435	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr1:223100040-223100190	AG09319	gingival:	n/a	n/a
18	MAFF	chr1:223099855-223100257	K562	blood:	n/a	chr1:223099950-223099968
19	CTCF	chr1:223100100-223100250	HPF	lung:	n/a	n/a
20	FOS	chr1:223100021-223100421	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:223099870-223100311	H1-neurons	neurons:	n/a	n/a
22	FOS	chr1:223099813-223100433	MCF10A-Er-Src	breast:	n/a	n/a
23	E2F4	chr1:223099996-223100294	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DISP1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1890615	0.81[ASN][1000 genomes]
rs1970382	0.83[ASN][1000 genomes]
rs2254329	0.81[ASN][1000 genomes]
rs2609343	0.81[ASN][1000 genomes]
rs2609384	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2609387	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2609391	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609392	0.80[ASN][1000 genomes]
rs2609393	0.80[ASN][1000 genomes]
rs2609394	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609396	0.80[ASN][1000 genomes]
rs2609397	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609398	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609404	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789960	0.80[ASN][1000 genomes]
rs2789962	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789963	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789964	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789965	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789968	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789969	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789971	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789973	0.83[ASN][1000 genomes]
rs2789974	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3101114	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873207	chr1:223078802-223292632	Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223083200-223101400	Weak transcription	Fetal Heart	heart
2	chr1:223083600-223101600	Weak transcription	Fetal Stomach	stomach
3	chr1:223090800-223101600	Weak transcription	Pancreas	Pancrea
4	chr1:223092400-223101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:223092400-223116200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:223093000-223101200	Weak transcription	Adipose Nuclei	Adipose
7	chr1:223094000-223101400	Weak transcription	HSMM	muscle
8	chr1:223095600-223101400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:223096000-223101400	Weak transcription	Fetal Kidney	kidney
10	chr1:223097200-223100200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:223097200-223101600	Weak transcription	Psoas Muscle	Psoas
12	chr1:223097400-223101200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:223097400-223101400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:223097400-223101400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:223097800-223101200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:223098000-223101200	Weak transcription	HepG2	liver
17	chr1:223098000-223101400	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:223098200-223101400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:223098400-223101000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:223098800-223101800	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:223098800-223101800	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:223099200-223100200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:223099200-223101000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:223099200-223101200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:223099200-223101600	Weak transcription	Left Ventricle	heart
26	chr1:223099400-223101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:223099800-223101400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:223099800-223101400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:223099800-223101400	Enhancers	Fetal Lung	lung
30	chr1:223099800-223101600	Enhancers	NHDF-Ad	bronchial
31	chr1:223099800-223101600	Enhancers	NHLF	lung
32	chr1:223099800-223102000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr1:223100000-223100200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:223100000-223100200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:223100000-223100200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:223100000-223100200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:223100000-223100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:223100000-223100200	Enhancers	Esophagus	oesophagus
39	chr1:223100000-223100200	Enhancers	Gastric	stomach
40	chr1:223100000-223100200	Flanking Active TSS	Ovary	ovary
41	chr1:223100000-223100400	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:223100000-223100400	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr1:223100000-223100400	Enhancers	Right Atrium	heart
44	chr1:223100000-223100400	Enhancers	HSMMtube	muscle
45	chr1:223100000-223100400	Flanking Active TSS	NHEK	skin
46	chr1:223100000-223100600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:223100000-223100600	Enhancers	Brain Germinal Matrix	brain
48	chr1:223100000-223100600	Enhancers	NH-A	brain
49	chr1:223100000-223100600	Enhancers	Osteobl	bone
50	chr1:223100000-223100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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