Variant report

Variant	rs6860627
Chromosome Location	chr5:111673187-111673188
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111672466..111674712-chr5:111689508..111691131,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11953449	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17134365	0.91[JPT][hapmap]
rs4958041	0.82[JPT][hapmap]
rs6594585	0.81[CEU][hapmap]
rs7706772	0.82[CEU][hapmap]
rs7714258	0.86[YRI][hapmap]
rs7718321	0.83[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821732	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861968	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs987767	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1021530	chr5:111626266-111683317	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1028181	chr5:111628901-111683317	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv462386	chr5:111667572-111699317	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv599372	chr5:111667572-111699317	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6860627	SNORA13	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111637400-111684600	Weak transcription	Aorta	Aorta
2	chr5:111653200-111674000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:111665400-111674600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:111665600-111674000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:111667200-111674000	Weak transcription	Esophagus	oesophagus
6	chr5:111669400-111673600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:111669400-111673600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:111669400-111674200	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:111669400-111674400	Enhancers	Fetal Heart	heart
10	chr5:111669400-111676000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:111669400-111678000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:111669600-111674000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:111669600-111674000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:111669600-111674200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:111669600-111674200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:111669600-111674200	Weak transcription	Adipose Nuclei	Adipose
17	chr5:111669600-111674200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:111669600-111674400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:111669600-111677800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:111669800-111673200	Weak transcription	Right Ventricle	heart
21	chr5:111669800-111673600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:111669800-111673600	Weak transcription	Pancreas	Pancrea
23	chr5:111669800-111673800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:111669800-111674000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:111669800-111674200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:111669800-111674200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:111669800-111674200	Weak transcription	Brain Substantia Nigra	brain
28	chr5:111669800-111674400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:111669800-111674400	Weak transcription	Fetal Lung	lung
30	chr5:111669800-111683600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:111670000-111675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr5:111670600-111673600	Weak transcription	HUVEC	blood vessel
33	chr5:111670600-111673800	Enhancers	Hela-S3	cervix
34	chr5:111671000-111673600	Weak transcription	Psoas Muscle	Psoas
35	chr5:111671200-111674200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:111671800-111674400	Weak transcription	Gastric	stomach
37	chr5:111672200-111673600	Weak transcription	Left Ventricle	heart
38	chr5:111672400-111674000	Weak transcription	Lung	lung
39	chr5:111672400-111674000	Weak transcription	Right Atrium	heart
40	chr5:111672800-111674000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:111673000-111675800	Enhancers	Skeletal Muscle Male	skeletal muscle

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