Variant report

Variant	rs2609402
Chromosome Location	chr1:223101088-223101089
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	chr1:223100840-223101196	SK-N-MC	brain:	n/a	n/a
2	TCF7L2	chr1:223100798-223101870	HEK293	kidney:	n/a	chr1:223101498-223101507 chr1:223101495-223101509 chr1:223101496-223101506 chr1:223101494-223101510 chr1:223101497-223101506 chr1:223101494-223101510

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];0.81[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];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609395	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609398	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609401	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];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789963	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789964	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789965	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789968	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789969	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789971	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789973	0.83[ASN][1000 genomes]
rs2789974	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3101114	0.88[AMR][1000 genomes];0.81[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: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	chr1:223098800-223101800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:223098800-223101800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:223099200-223101200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:223099200-223101600	Weak transcription	Left Ventricle	heart
22	chr1:223099400-223101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:223099800-223101400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:223099800-223101400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:223099800-223101400	Enhancers	Fetal Lung	lung
26	chr1:223099800-223101600	Enhancers	NHDF-Ad	bronchial
27	chr1:223099800-223101600	Enhancers	NHLF	lung
28	chr1:223099800-223102000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:223100000-223101400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:223100200-223101200	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:223100200-223101600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:223100200-223101600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:223100200-223101600	Weak transcription	Esophagus	oesophagus
34	chr1:223100200-223101600	Weak transcription	Gastric	stomach
35	chr1:223100200-223101800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:223100200-223101800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr1:223100200-223116200	Weak transcription	Fetal Intestine Small	intestine
38	chr1:223100400-223101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:223100400-223101400	Enhancers	Colon Smooth Muscle	Colon
40	chr1:223100400-223101400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:223100400-223101400	Enhancers	NHEK	skin
42	chr1:223100400-223101600	Weak transcription	Right Atrium	heart
43	chr1:223100400-223104400	Weak transcription	HSMMtube	muscle
44	chr1:223100600-223101200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:223100600-223101200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:223100600-223101400	Weak transcription	Ovary	ovary
47	chr1:223100600-223101600	Weak transcription	NH-A	brain
48	chr1:223100600-223101800	Weak transcription	Osteobl	bone
49	chr1:223100600-223102200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:223100800-223101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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