Variant report

Variant	rs7722612
Chromosome Location	chr5:177826469-177826470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10038165	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11738251	0.84[ASN][1000 genomes]
rs12658831	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12659358	0.84[EUR][1000 genomes]
rs2910125	0.90[JPT][hapmap]
rs2973735	0.81[ASN][1000 genomes]
rs2973737	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2973738	0.84[EUR][1000 genomes]
rs2973741	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4357053	0.85[ASN][1000 genomes]
rs4615316	0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4976773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976774	0.96[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4976775	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59008505	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72822867	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv1027165	chr5:177693601-177843314	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv1796529	chr5:177804032-177840382	Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1817842	chr5:177804032-177840382	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv1836928	chr5:177804032-177840382	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv1837218	chr5:177804032-177840382	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv600399	chr5:177807623-177830769	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv600416	chr5:177822001-177830605	Bivalent Enhancer Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7722612	COL23A1	cis	cerebellum	SCAN
rs7722612	PRR7	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177824200-177827200	Enhancers	Fetal Thymus	thymus
2	chr5:177825600-177827000	Bivalent Enhancer	Fetal Stomach	stomach
3	chr5:177825800-177826600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:177825800-177826600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:177825800-177826600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr5:177825800-177826600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:177825800-177826800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:177825800-177827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:177825800-177827000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:177825800-177827000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr5:177825800-177827000	Enhancers	Thymus	Thymus
12	chr5:177826000-177826600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr5:177826000-177826600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:177826000-177826600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr5:177826000-177826600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr5:177826000-177826600	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr5:177826000-177826600	Bivalent Enhancer	Placenta	Placenta
18	chr5:177826000-177826800	Enhancers	Fetal Lung	lung
19	chr5:177826400-177826600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr5:177826400-177826600	Enhancers	HSMMtube	muscle

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