Variant report

Variant	rs2789962
Chromosome Location	chr1:223097150-223097151
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:223097080-223097230	HPF	lung:	n/a	n/a
2	CTCF	chr1:223097040-223097190	HVMF	connective:	n/a	n/a
3	CTCF	chr1:223097000-223097150	HBMEC	blood vessel:	n/a	n/a
4	CTCF	chr1:223097000-223097150	HPF	lung:	n/a	n/a
5	RAD21	chr1:223097036-223097217	IMR90	lung:	n/a	n/a
6	CTCF	chr1:223097000-223097150	HPAF	blood vessel:	n/a	n/a
7	CTCF	chr1:223097020-223097170	AG04450	lung:	n/a	n/a
8	CTCF	chr1:223097040-223097190	HBMEC	blood vessel:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223093236..223095130-chr1:223096668..223099706,3	K562	blood:
2	chr1:223092526..223094736-chr1:223096745..223098289,2	K562	blood:

No data

Variant related genes	Relation type
DISP1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17163572	0.95[YRI][hapmap]
rs1890615	0.80[ASN][1000 genomes]
rs1970382	0.81[ASN][1000 genomes]
rs2254329	0.80[ASN][1000 genomes]
rs2609343	0.80[ASN][1000 genomes]
rs2609384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2609387	0.94[ASN][1000 genomes]
rs2609388	0.84[JPT][hapmap]
rs2609391	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2609392	0.81[ASN][1000 genomes]
rs2609393	0.81[ASN][1000 genomes]
rs2609394	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609395	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609396	0.81[ASN][1000 genomes]
rs2609397	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609400	0.84[JPT][hapmap]
rs2609401	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609402	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609406	0.84[JPT][hapmap]
rs2609408	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789960	0.81[ASN][1000 genomes]
rs2789963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789965	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789966	0.84[JPT][hapmap]
rs2789967	0.84[JPT][hapmap]
rs2789968	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789969	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789970	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789971	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789973	0.82[ASN][1000 genomes]
rs2789974	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3101114	0.86[AMR][1000 genomes];0.94[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:37 , 50 per page) page: 1

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	chr1:223092400-223098600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:223092400-223101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:223092400-223116200	Weak transcription	Primary B cells from cord blood	blood
7	chr1:223093000-223097200	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:223093000-223097400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:223093000-223101200	Weak transcription	Adipose Nuclei	Adipose
10	chr1:223094000-223099800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:223094000-223099800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:223094000-223101400	Weak transcription	HSMM	muscle
13	chr1:223094600-223099800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:223094800-223097400	Enhancers	Stomach Mucosa	stomach
15	chr1:223095000-223098000	Enhancers	Fetal Lung	lung
16	chr1:223095400-223098000	Enhancers	Ovary	ovary
17	chr1:223095600-223099000	Weak transcription	Right Atrium	heart
18	chr1:223095600-223100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:223095600-223101400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:223095800-223097600	Weak transcription	Osteobl	bone
21	chr1:223096000-223097200	Weak transcription	HepG2	liver
22	chr1:223096000-223101400	Weak transcription	Fetal Kidney	kidney
23	chr1:223096400-223098200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:223096600-223097200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr1:223096600-223097200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:223096600-223097400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:223096600-223098200	Enhancers	Colon Smooth Muscle	Colon
28	chr1:223096800-223097200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr1:223096800-223098200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:223096800-223099600	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:223097000-223097200	Enhancers	Psoas Muscle	Psoas
32	chr1:223097000-223097200	Bivalent Enhancer	NHDF-Ad	bronchial
33	chr1:223097000-223097600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:223097000-223097800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:223097000-223097800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:223097000-223097800	Enhancers	NHLF	lung
37	chr1:223097000-223098400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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