Variant report

Variant	rs2030558
Chromosome Location	chr1:175889627-175889628
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr1:175889384-175890023	IMR90	lung:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RFWD2-1	chr1:175889592-175889649	XLOC_001099

Variant related genes	Relation type
ENSG00000230777	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11584930	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801359	0.89[EUR][1000 genomes]
rs12405136	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12729379	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12732415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12753832	0.87[MEX][hapmap]
rs34441614	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656281	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545971	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs954978	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33328	chr1:175446583-175910001	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2030558	SNORD78	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175863200-175906400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:175874400-175945600	Weak transcription	A549	lung
3	chr1:175877400-175894600	Weak transcription	HSMM	muscle
4	chr1:175877800-175902400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:175879800-175896000	Weak transcription	Fetal Stomach	stomach
6	chr1:175880000-175897200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:175880000-175897400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:175880000-175937800	Weak transcription	HSMMtube	muscle
9	chr1:175880400-175891800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:175880400-175904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:175880600-175896200	Weak transcription	Placenta	Placenta
12	chr1:175880600-175896400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:175881000-175897200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:175881000-175905200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:175881000-175924200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:175881200-175894800	Weak transcription	Primary T cells from cord blood	blood
17	chr1:175881400-175893400	Weak transcription	GM12878-XiMat	blood
18	chr1:175881400-175894800	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:175881400-175896600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:175881400-175897400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:175882000-175895000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:175882600-175894600	Weak transcription	Fetal Brain Female	brain
23	chr1:175882600-175895600	Weak transcription	Lung	lung
24	chr1:175882600-175902200	Weak transcription	Aorta	Aorta
25	chr1:175882600-175910200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:175883200-175895000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:175883200-175908200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:175884200-175897400	Weak transcription	Pancreas	Pancrea
29	chr1:175885800-175896400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:175885800-175897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:175885800-175897400	Weak transcription	Left Ventricle	heart
32	chr1:175886000-175895000	Weak transcription	Ovary	ovary
33	chr1:175886200-175896200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:175886400-175929400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:175886800-175890800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:175887600-175895000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:175887800-175896400	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:175887800-175929800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:175888000-175890000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:175888000-175890600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:175888200-175890600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
42	chr1:175888600-175889800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:175889200-175889800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:175889200-175889800	Enhancers	Small Intestine	intestine
45	chr1:175889200-175890800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
46	chr1:175889200-175937800	Weak transcription	Osteobl	bone
47	chr1:175889400-175890000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:175889400-175890000	Strong transcription	Brain Germinal Matrix	brain
49	chr1:175889400-175891200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr1:175889400-175896800	Weak transcription	Fetal Lung	lung

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