Variant report

Variant	rs2789948
Chromosome Location	chr1:223184459-223184460
allele	G/T
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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255147	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2609351	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2609352	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2609353	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2609355	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789912	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789949	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2789951	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2971990	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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
rs2789948	ESRRG	cis	parietal	SCAN
rs2789948	NVL	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

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	chr1:223177200-223184600	Weak transcription	Psoas Muscle	Psoas
4	chr1:223177200-223189800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:223178000-223184600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:223178200-223184600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:223178200-223184600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:223178800-223184600	Weak transcription	Aorta	Aorta
9	chr1:223178800-223184600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:223178800-223186800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:223178800-223189600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:223178800-223191400	Weak transcription	Right Atrium	heart
13	chr1:223178800-223194600	Weak transcription	Gastric	stomach
14	chr1:223179000-223184600	Weak transcription	Left Ventricle	heart
15	chr1:223179000-223184600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:223179000-223189800	Weak transcription	Right Ventricle	heart
17	chr1:223179000-223190200	Weak transcription	Adipose Nuclei	Adipose
18	chr1:223179200-223189800	Weak transcription	Lung	lung
19	chr1:223179200-223195400	Weak transcription	Spleen	Spleen
20	chr1:223180200-223184600	Weak transcription	Fetal Intestine Large	intestine
21	chr1:223180200-223184800	Enhancers	Colon Smooth Muscle	Colon
22	chr1:223180600-223185600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:223180800-223186200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:223181000-223189600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:223181200-223184600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:223181600-223184600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:223181800-223186000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:223182600-223185200	Enhancers	Brain Germinal Matrix	brain
29	chr1:223182800-223185800	Enhancers	Fetal Muscle Leg	muscle
30	chr1:223183200-223184600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:223183200-223184600	Enhancers	Liver	Liver
32	chr1:223183400-223184600	Weak transcription	Fetal Lung	lung
33	chr1:223183400-223184600	Weak transcription	Ovary	ovary
34	chr1:223183600-223185000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr1:223183600-223185000	Enhancers	Fetal Stomach	stomach
36	chr1:223183600-223185200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:223183600-223185200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:223183800-223185200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:223184000-223184800	Enhancers	Stomach Mucosa	stomach
40	chr1:223184000-223185000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:223184000-223185000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:223184200-223184600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:223184200-223184800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:223184200-223184800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr1:223184200-223184800	Active TSS	HSMMtube	muscle
46	chr1:223184200-223184800	Enhancers	NH-A	brain
47	chr1:223184200-223185000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:223184200-223185000	Enhancers	H9 Cell Line	embryonic stem cell
49	chr1:223184200-223185000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:223184200-223185000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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