Variant report

Variant	rs6675208
Chromosome Location	chr1:180300936-180300937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1072856	1.00[EUR][1000 genomes]
rs16855661	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855695	0.85[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855749	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855769	1.00[EUR][1000 genomes]
rs16855834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855850	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855855	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855910	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855982	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855986	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16855990	1.00[EUR][1000 genomes]
rs16856007	1.00[ASW][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856037	0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16856064	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2764454	0.81[MKK][hapmap]
rs4590641	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55675122	1.00[EUR][1000 genomes]
rs55698496	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55719709	1.00[EUR][1000 genomes]
rs55754938	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56005059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56089354	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56128856	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56233435	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56246577	1.00[EUR][1000 genomes]
rs56376445	1.00[EUR][1000 genomes]
rs57451284	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57948698	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58175505	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59566983	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59612061	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60088677	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60300532	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60439251	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60509208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60729009	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60923108	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60993519	1.00[EUR][1000 genomes]
rs61057572	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61700262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6672551	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6675201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132445	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132456	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132463	1.00[EUR][1000 genomes]
rs74132465	1.00[EUR][1000 genomes]
rs74132472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132478	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132803	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74132903	1.00[EUR][1000 genomes]
rs74132904	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132915	1.00[EUR][1000 genomes]
rs74132919	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74132933	1.00[EUR][1000 genomes]
rs74135059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74135188	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518809	1.00[EUR][1000 genomes]
rs7518923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7520598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7536470	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7537732	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7548328	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9659140	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS 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	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS 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	39 gene(s)	inside rSNPs	diseases
6	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
7	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
8	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180281000-180329400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:180282800-180313400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:180283000-180302800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:180283000-180302800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:180294400-180303000	Weak transcription	Placenta	Placenta
6	chr1:180295800-180302600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:180295800-180309200	Weak transcription	Primary B cells from cord blood	blood
8	chr1:180296200-180302600	Weak transcription	Pancreas	Pancrea
9	chr1:180296400-180302400	Weak transcription	Dnd41	blood
10	chr1:180296600-180301200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:180296600-180302600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:180296600-180309000	Weak transcription	Primary T cells from cord blood	blood
13	chr1:180300400-180301200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:180300400-180309200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:180300600-180301200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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