Variant report

Variant	rs6825601
Chromosome Location	chr4:122116998-122116999
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	chr4:122116938-122117335	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr4:122116868-122117280	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
RNU6-948P	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10000692	0.94[YRI][hapmap]
rs10004021	0.94[YRI][hapmap]
rs10009822	1.00[AMR][1000 genomes]
rs10017221	1.00[AMR][1000 genomes]
rs10021787	0.94[YRI][hapmap];0.83[AMR][1000 genomes]
rs11938699	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17051305	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17051318	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051319	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28452005	0.83[AMR][1000 genomes]
rs28452943	1.00[AMR][1000 genomes]
rs28567402	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28572759	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28600934	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28669888	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28707603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6534255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6534256	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6817294	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6840309	0.83[AMR][1000 genomes]
rs6845343	0.83[AMR][1000 genomes]
rs6847595	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847834	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6847971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6849687	1.00[MEX][hapmap]
rs6852366	1.00[MEX][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes]
rs7682759	0.94[YRI][hapmap];0.83[AMR][1000 genomes]
rs7684215	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7684241	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs7684464	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7684586	0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9784553	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9992473	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9992978	1.00[AMR][1000 genomes]
rs9995558	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1009395	chr4:121841442-122557363	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv537235	chr4:121841442-122557363	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3386870	chr4:121867625-122208448	Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879859	chr4:121892490-122438312	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879860	chr4:122030864-122126808	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122113800-122119600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr4:122114000-122119600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:122114000-122120600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:122114400-122120400	Weak transcription	Primary T cells from cord blood	blood
5	chr4:122114600-122119800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr4:122114800-122119400	Weak transcription	GM12878-XiMat	blood
7	chr4:122115000-122119600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:122115200-122120400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:122116800-122117200	Enhancers	Fetal Lung	lung
10	chr4:122116800-122117400	Enhancers	Fetal Heart	heart

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