Variant report

Variant	rs220419
Chromosome Location	chr6:86862204-86862205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1107192	0.81[ASN][1000 genomes]
rs1334640	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1334649	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1413722	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1556626	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2151987	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2151989	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs220391	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs220411	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs220413	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs220415	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35318177	0.83[ASN][1000 genomes]
rs4707258	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6454528	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6908579	0.81[ASN][1000 genomes]
rs6921250	0.81[EUR][1000 genomes]
rs9359686	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022618	chr6:86465365-87432069	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv538352	chr6:86465365-87432069	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1027719	chr6:86745200-87326311	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1026234	chr6:86745200-87640200	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv532046	chr6:86754494-87615799	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv1024339	chr6:86778852-87622650	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1018878	chr6:86778852-87691755	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1029725	chr6:86790883-87363024	Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1017246	chr6:86815397-87354355	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1031639	chr6:86815397-87721507	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv1019356	chr6:86826097-86919420	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3416130	chr6:86837282-86864146	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs220419	LYRM2	cis	cerebellum	SCAN
rs220419	SNORD50A	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86854800-86865800	Weak transcription	Ovary	ovary
2	chr6:86860800-86862600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:86861200-86862600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:86861400-86862400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:86861400-86862800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr6:86861400-86862800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr6:86861600-86862600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:86861800-86862600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:86861800-86862800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:86862000-86863000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:86862200-86862600	Enhancers	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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