Variant report

Variant	rs2789951
Chromosome Location	chr1:223186683-223186684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1048209	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255147	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2609351	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609352	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2609353	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2609355	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789912	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789948	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789949	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2971990	0.98[AMR][1000 genomes];0.98[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	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
5	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
6	nsv917330	chr1:223141547-223225893	Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2789951	NVL	cis	parietal	SCAN
rs2789951	ESRRG	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223169000-223187600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:223175200-223189800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:223177200-223189800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:223178800-223186800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:223178800-223189600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:223178800-223191400	Weak transcription	Right Atrium	heart
7	chr1:223178800-223194600	Weak transcription	Gastric	stomach
8	chr1:223179000-223189800	Weak transcription	Right Ventricle	heart
9	chr1:223179000-223190200	Weak transcription	Adipose Nuclei	Adipose
10	chr1:223179200-223189800	Weak transcription	Lung	lung
11	chr1:223179200-223195400	Weak transcription	Spleen	Spleen
12	chr1:223181000-223189600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:223184800-223204800	Weak transcription	Stomach Mucosa	stomach
14	chr1:223185000-223186800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:223185000-223187400	Weak transcription	Fetal Kidney	kidney
16	chr1:223185000-223188400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:223185000-223189800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:223185000-223196800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:223185200-223187400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:223185200-223188000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:223185200-223188400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:223185200-223188400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:223185200-223189000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:223185200-223189800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:223185200-223189800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:223185200-223189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:223185200-223190600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:223185200-223196000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:223185400-223190400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:223185600-223187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:223185600-223189600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:223186000-223186800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:223186200-223186800	Enhancers	Colon Smooth Muscle	Colon
34	chr1:223186200-223193200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:223186600-223186800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:223186600-223192200	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:223186600-223195400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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