Variant report

Variant	rs2609399
Chromosome Location	chr1:223098549-223098550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10495205	0.81[AFR][1000 genomes]
rs17163548	0.81[ASN][1000 genomes]
rs17163550	0.81[ASN][1000 genomes]
rs17163557	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17163559	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17163564	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609382	0.82[AFR][1000 genomes]
rs2609385	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2609386	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2609388	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2609390	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2609400	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609403	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609405	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609406	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2609407	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789961	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789966	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789967	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2789975	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35185132	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73128670	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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:38 , 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	chr1:223093000-223101200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:223094000-223099800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:223094000-223099800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:223094000-223101400	Weak transcription	HSMM	muscle
11	chr1:223094600-223099800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:223095600-223099000	Weak transcription	Right Atrium	heart
13	chr1:223095600-223100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:223095600-223101400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:223096000-223101400	Weak transcription	Fetal Kidney	kidney
16	chr1:223096800-223099600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:223097200-223098800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:223097200-223100200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:223097200-223101600	Weak transcription	Psoas Muscle	Psoas
20	chr1:223097400-223098800	Weak transcription	Stomach Mucosa	stomach
21	chr1:223097400-223099200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr1:223097400-223101200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:223097400-223101400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:223097400-223101400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:223097600-223098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:223097800-223098800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:223097800-223099800	Weak transcription	NHLF	lung
28	chr1:223097800-223101200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:223098000-223099800	Weak transcription	Fetal Lung	lung
30	chr1:223098000-223100000	Weak transcription	Ovary	ovary
31	chr1:223098000-223100000	Weak transcription	Osteobl	bone
32	chr1:223098000-223101200	Weak transcription	HepG2	liver
33	chr1:223098000-223101400	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:223098200-223099800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:223098200-223099800	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:223098200-223101400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:223098400-223098800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:223098400-223101000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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