Variant report

Variant	rs3888104
Chromosome Location	chr1:197394090-197394091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197393861..197396014-chr1:197399559..197401986,3	K562	blood:
2	chr1:197385261..197387512-chr1:197393443..197395801,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1022908	1.00[AMR][1000 genomes]
rs1033826	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494753	0.87[AMR][1000 genomes]
rs10801606	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10922235	1.00[AMR][1000 genomes]
rs12089070	0.87[AMR][1000 genomes]
rs1421390	1.00[AMR][1000 genomes]
rs1421391	1.00[AMR][1000 genomes]
rs1421394	1.00[AMR][1000 genomes]
rs1570412	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1570413	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1592707	1.00[AMR][1000 genomes]
rs1592708	1.00[AMR][1000 genomes]
rs1923758	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1923760	1.00[YRI][hapmap]
rs1923761	0.98[AFR][1000 genomes]
rs1923763	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs1951697	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1998433	1.00[AMR][1000 genomes]
rs2146484	0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2146485	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160967	1.00[AMR][1000 genomes]
rs2181373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256222	0.93[YRI][hapmap]
rs2359119	0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2476016	0.94[AFR][1000 genomes]
rs2476017	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2476018	0.93[YRI][hapmap]
rs2476022	0.98[AFR][1000 genomes]
rs2476024	0.87[AFR][1000 genomes]
rs2494272	0.98[AFR][1000 genomes]
rs2759660	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2821099	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2821100	0.98[AFR][1000 genomes]
rs2821105	0.92[YRI][hapmap]
rs3902057	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244150	0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4335404	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4428919	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs4989560	1.00[AMR][1000 genomes]
rs6428401	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6428402	1.00[AMR][1000 genomes]
rs6428403	0.87[AMR][1000 genomes]
rs6428405	1.00[AMR][1000 genomes]
rs6428406	1.00[AMR][1000 genomes]
rs6656674	1.00[AMR][1000 genomes]
rs6664766	1.00[AMR][1000 genomes]
rs6670147	1.00[AMR][1000 genomes]
rs6678776	0.87[AMR][1000 genomes]
rs6684593	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6686241	1.00[AMR][1000 genomes]
rs6689739	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690015	0.87[AMR][1000 genomes]
rs6691940	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694254	1.00[AMR][1000 genomes]
rs7514167	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7515749	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7525737	0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs7530158	1.00[AMR][1000 genomes]
rs927511	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs942050	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9427667	0.91[AFR][1000 genomes]
rs980370	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs980371	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197388800-197407000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:197388800-197407000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:197389600-197405800	Weak transcription	Brain Germinal Matrix	brain
4	chr1:197391600-197398400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:197392800-197394200	Enhancers	Fetal Lung	lung
6	chr1:197394000-197394800	Weak transcription	Hela-S3	cervix

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