Variant report

Variant	rs628857
Chromosome Location	chr5:178014668-178014669
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11249553	0.84[AMR][1000 genomes]
rs11737903	0.92[CEU][hapmap]
rs11747742	0.92[CEU][hapmap]
rs13155255	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs13156622	0.92[CEU][hapmap]
rs262027	0.82[AMR][1000 genomes]
rs35460909	0.84[AMR][1000 genomes]
rs3925518	0.89[JPT][hapmap]
rs4976738	0.83[JPT][hapmap]
rs501721	0.92[CEU][hapmap];0.86[AMR][1000 genomes]
rs519984	0.86[AMR][1000 genomes]
rs530542	0.87[AMR][1000 genomes]
rs540354	0.87[ASN][1000 genomes]
rs543862	0.81[CEU][hapmap]
rs555417	0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs565978	0.87[ASN][1000 genomes]
rs574103	0.87[AMR][1000 genomes]
rs576097	0.81[AMR][1000 genomes]
rs584415	0.86[AMR][1000 genomes]
rs596780	0.92[CEU][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes]
rs602451	0.92[CEU][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes]
rs643936	0.87[AMR][1000 genomes]
rs649585	0.86[AMR][1000 genomes]
rs6883747	0.89[JPT][hapmap]
rs6886390	0.86[AMR][1000 genomes]
rs721144	0.86[AMR][1000 genomes]
rs7700943	0.81[CEU][hapmap]
rs7724406	0.81[CEU][hapmap]
rs7732660	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883216	chr5:178002325-178025087	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs628857	MGAT4B	cis	cerebellum	SCAN
rs628857	CLK4	cis	lesional skin	skin_eQTL
rs628857	CLK4	cis	cerebellum	SCAN
rs628857	RMND5B	cis	cerebellum	SCAN
rs628857	CLK4	cis	normal skin	skin_eQTL
rs628857	FLT4	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178012800-178014800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:178012800-178014800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:178012800-178014800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:178012800-178014800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:178012800-178015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:178012800-178015000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:178012800-178015000	Enhancers	Fetal Stomach	stomach
8	chr5:178012800-178015000	Weak transcription	Lung	lung
9	chr5:178012800-178016600	Weak transcription	Right Atrium	heart
10	chr5:178012800-178016800	Weak transcription	Gastric	stomach
11	chr5:178013200-178015600	Bivalent Enhancer	Fetal Lung	lung
12	chr5:178013200-178016000	Weak transcription	Pancreas	Pancrea
13	chr5:178013800-178014800	Enhancers	Brain Hippocampus Middle	brain
14	chr5:178013800-178015600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:178014200-178014800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:178014200-178015000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr5:178014200-178016600	Bivalent Enhancer	Fetal Heart	heart
18	chr5:178014400-178014800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:178014400-178015000	Enhancers	Brain Angular Gyrus	brain
20	chr5:178014400-178015400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:178014400-178015800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:178014600-178015800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr5:178014600-178015800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
24	chr5:178014600-178018000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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