Variant report

Variant	rs2817051
Chromosome Location	chr6:35731702-35731703
allele	C/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	POLR2A	chr6:35731562-35731844	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:35731633-35731704	GM13976	blood:	n/a	n/a
3	POLR2A	chr6:35731215-35732878	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:35731475-35732511	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000220734	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2263331	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2766556	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766557	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2766558	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2766560	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2766561	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2766562	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2766563	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2766564	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2766565	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2766567	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2766570	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2817045	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2817047	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817048	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817049	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817050	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2817053	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817054	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2817055	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817057	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817058	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817060	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817061	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457848	0.87[ASN][1000 genomes]
rs7768547	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366891	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394316	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9470089	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv885805	chr6:35685955-35779879	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2817051	GLP1R	cis	cerebellum	SCAN
rs2817051	HLA-DRB5	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35716600-35732200	Weak transcription	Right Atrium	heart
2	chr6:35725800-35731800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:35726200-35732000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:35731200-35731800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:35731200-35731800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:35731200-35731800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:35731200-35732000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:35731200-35732600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:35731400-35731800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:35731400-35731800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:35731400-35732400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:35731400-35732600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:35731400-35732600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:35731600-35731800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:35731600-35731800	Bivalent Enhancer	Primary T cells from cord blood	blood
16	chr6:35731600-35732000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:35731600-35732000	Bivalent Enhancer	Fetal Brain Female	brain
18	chr6:35731600-35732600	Active TSS	H1 Cell Line	embryonic stem cell
19	chr6:35731600-35732600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:35731600-35732600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:35731600-35732600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:35731600-35733000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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