Variant report

Variant	rs2789966
Chromosome Location	chr1:223100293-223100294
allele	G/T
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	STAT3	chr1:223100039-223100329	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr1:223099835-223100468	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr1:223099861-223100417	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr1:223099937-223100425	MCF10A-Er-Src	breast:	n/a	n/a
6	RAD21	chr1:223099985-223100342	H1-hESC	embryonic stem cell:	n/a	n/a
7	STAT3	chr1:223100078-223100322	MCF10A-Er-Src	breast:	n/a	n/a
8	RAD21	chr1:223100110-223100369	H1-hESC	embryonic stem cell:	n/a	n/a
9	MYC	chr1:223099975-223100435	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:223100021-223100421	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:223099870-223100311	H1-neurons	neurons:	n/a	n/a
12	FOS	chr1:223099813-223100433	MCF10A-Er-Src	breast:	n/a	n/a
13	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]
rs10495205	1.00[ASW][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap]
rs17162913	0.82[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap]
rs17163550	0.81[AFR][1000 genomes]
rs17163557	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163559	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163564	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609382	0.81[AFR][1000 genomes]
rs2609384	0.84[JPT][hapmap]
rs2609385	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609386	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609388	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609390	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609391	0.84[JPT][hapmap]
rs2609398	0.84[JPT][hapmap]
rs2609399	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609403	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609405	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609406	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609407	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609408	0.84[JPT][hapmap]
rs2789961	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789962	0.84[JPT][hapmap]
rs2789967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789970	0.84[JPT][hapmap]
rs2789975	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34715037	0.82[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap]
rs35185132	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73128670	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:54 , 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	chr1:223097200-223101600	Weak transcription	Psoas Muscle	Psoas
11	chr1:223097400-223101200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:223097400-223101400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:223097400-223101400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:223097800-223101200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:223098000-223101200	Weak transcription	HepG2	liver
16	chr1:223098000-223101400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:223098200-223101400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:223098400-223101000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:223098800-223101800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:223098800-223101800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr1:223099200-223101000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:223099200-223101200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:223099200-223101600	Weak transcription	Left Ventricle	heart
24	chr1:223099400-223101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:223099800-223101400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:223099800-223101400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:223099800-223101400	Enhancers	Fetal Lung	lung
28	chr1:223099800-223101600	Enhancers	NHDF-Ad	bronchial
29	chr1:223099800-223101600	Enhancers	NHLF	lung
30	chr1:223099800-223102000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:223100000-223100400	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:223100000-223100400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:223100000-223100400	Enhancers	Right Atrium	heart
34	chr1:223100000-223100400	Enhancers	HSMMtube	muscle
35	chr1:223100000-223100400	Flanking Active TSS	NHEK	skin
36	chr1:223100000-223100600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:223100000-223100600	Enhancers	Brain Germinal Matrix	brain
38	chr1:223100000-223100600	Enhancers	NH-A	brain
39	chr1:223100000-223100600	Enhancers	Osteobl	bone
40	chr1:223100000-223100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:223100000-223100800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:223100000-223100800	Enhancers	Liver	Liver
43	chr1:223100000-223101400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:223100200-223100400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:223100200-223100600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:223100200-223100600	Active TSS	Ovary	ovary
47	chr1:223100200-223101200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:223100200-223101600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:223100200-223101600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:223100200-223101600	Weak transcription	Esophagus	oesophagus

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