Variant report

Variant	rs2609391
Chromosome Location	chr1:223111708-223111709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17163572	0.89[GIH][hapmap]
rs2609384	0.89[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];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609387	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609388	0.84[JPT][hapmap]
rs2609394	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2609395	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2609397	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2609398	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]
rs2609400	0.84[JPT][hapmap]
rs2609401	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609402	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609404	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609406	0.84[JPT][hapmap]
rs2609408	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];0.96[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789962	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]
rs2789963	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2789964	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2789965	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2789966	0.84[JPT][hapmap]
rs2789967	0.84[JPT][hapmap]
rs2789968	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789969	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789970	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];0.96[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789971	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2789974	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3101114	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997861	0.82[AMR][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	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
7	esv1828950	chr1:223111708-223132433	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223092400-223116200	Weak transcription	Primary B cells from cord blood	blood
2	chr1:223100200-223116200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:223102000-223113600	Weak transcription	Left Ventricle	heart
4	chr1:223102000-223116200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:223102200-223116000	Weak transcription	Placenta	Placenta
6	chr1:223102200-223116200	Weak transcription	Fetal Stomach	stomach
7	chr1:223102200-223116200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:223102200-223119400	Weak transcription	NHLF	lung
9	chr1:223102200-223128000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:223102200-223130800	Weak transcription	Fetal Brain Male	brain
11	chr1:223102400-223121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:223102600-223117800	Weak transcription	Psoas Muscle	Psoas
13	chr1:223102600-223121200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:223102800-223116200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:223102800-223124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:223103200-223116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:223103800-223116200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:223104400-223116200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:223105000-223116400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:223105000-223128800	Weak transcription	Ovary	ovary
21	chr1:223105200-223118400	Weak transcription	HSMMtube	muscle
22	chr1:223105400-223115000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:223105400-223116400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:223105400-223119000	Weak transcription	Right Atrium	heart
25	chr1:223105600-223112200	Weak transcription	Fetal Lung	lung
26	chr1:223106200-223116200	Weak transcription	Stomach Mucosa	stomach
27	chr1:223108000-223120600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:223109200-223116200	Weak transcription	Right Ventricle	heart
29	chr1:223109600-223114400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:223109600-223116200	Weak transcription	Liver	Liver
31	chr1:223109600-223116200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:223109800-223114200	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:223111200-223112400	Weak transcription	Fetal Kidney	kidney
34	chr1:223111400-223116200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:223111400-223116200	Weak transcription	Brain Anterior Caudate	brain
36	chr1:223111600-223122800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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