Variant report

Variant	rs6941417
Chromosome Location	chr6:25152674-25152675
allele	A/G
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	chr6:25152672-25152797	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000262400	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10946752	0.88[ASN][1000 genomes]
rs11752102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663706	0.83[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16890179	0.88[CEU][hapmap];0.85[JPT][hapmap]
rs1900554	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4712889	0.99[ASN][1000 genomes]
rs6909903	0.82[ASN][1000 genomes]
rs6910965	0.82[CEU][hapmap]
rs6915489	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6922783	0.90[ASN][1000 genomes]
rs7748381	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348664	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356963	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9356964	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366606	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379723	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379726	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393620	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393621	0.89[ASN][1000 genomes]
rs9461115	0.83[ASN][1000 genomes]
rs9467430	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6941417	CMAH	cis	lymphoblastoid	seeQTL
rs6941417	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs6941417	CMAH	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25138800-25152800	Weak transcription	Lung	lung
2	chr6:25139200-25154800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:25139600-25152800	Weak transcription	Thymus	Thymus
4	chr6:25143400-25154600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:25150200-25154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr6:25150200-25155200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25150400-25155400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:25150600-25155000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:25151200-25153200	Strong transcription	Fetal Thymus	thymus
10	chr6:25151200-25153400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:25151200-25155600	Weak transcription	Right Atrium	heart
12	chr6:25151800-25152800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:25152400-25153000	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr6:25152400-25153000	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr6:25152600-25152800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:25152600-25153200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:25152600-25155200	Genic enhancers	Dnd41	blood

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