Variant report

Variant	rs2609406
Chromosome Location	chr1:223104829-223104830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10495205	0.82[ASW][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs17162913	0.94[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.81[YRI][hapmap]
rs17163557	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163564	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609382	0.84[AFR][1000 genomes]
rs2609384	0.84[JPT][hapmap]
rs2609385	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609386	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609390	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2609391	0.84[JPT][hapmap]
rs2609398	0.84[JPT][hapmap]
rs2609399	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609400	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609405	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609407	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609408	0.84[JPT][hapmap]
rs2789961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2789962	0.84[JPT][hapmap]
rs2789966	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]
rs2789967	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789970	0.84[JPT][hapmap]
rs2789975	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34715037	0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[YRI][hapmap]
rs35185132	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73128670	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9651262	0.87[YRI][hapmap]

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:42 , 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	chr1:223101800-223105400	Active TSS	Right Atrium	heart
4	chr1:223102000-223113600	Weak transcription	Left Ventricle	heart
5	chr1:223102000-223116200	Weak transcription	Brain Substantia Nigra	brain
6	chr1:223102200-223106800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:223102200-223116000	Weak transcription	Placenta	Placenta
8	chr1:223102200-223116200	Weak transcription	Fetal Stomach	stomach
9	chr1:223102200-223116200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:223102200-223119400	Weak transcription	NHLF	lung
11	chr1:223102200-223128000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:223102200-223130800	Weak transcription	Fetal Brain Male	brain
13	chr1:223102400-223106200	Weak transcription	NHEK	skin
14	chr1:223102400-223121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:223102600-223109000	Weak transcription	Right Ventricle	heart
16	chr1:223102600-223109200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:223102600-223117800	Weak transcription	Psoas Muscle	Psoas
18	chr1:223102600-223121200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:223102800-223116200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:223102800-223124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:223103000-223105600	Enhancers	Fetal Lung	lung
22	chr1:223103200-223116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:223103400-223105000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:223103600-223105400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:223103600-223105600	Enhancers	Colon Smooth Muscle	Colon
26	chr1:223103800-223105600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:223103800-223116200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:223104200-223105000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:223104200-223105000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:223104200-223105000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:223104200-223105000	Enhancers	Osteobl	bone
32	chr1:223104200-223105400	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:223104400-223105000	Enhancers	Fetal Kidney	kidney
34	chr1:223104400-223105200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr1:223104400-223105200	Enhancers	HSMMtube	muscle
36	chr1:223104400-223116200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:223104600-223105000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:223104600-223105000	Enhancers	Ovary	ovary
39	chr1:223104600-223105000	Enhancers	HSMM	muscle
40	chr1:223104600-223105200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:223104600-223105400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:223104800-223106200	Enhancers	Stomach Mucosa	stomach

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