Variant report

Variant	rs10419827
Chromosome Location	chr19:42306984-42306985
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	chr19:42295737..42298028-chr19:42304935..42307847,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10401370	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10401528	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10401928	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407206	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10407619	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10407797	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10408367	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10410918	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10414823	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10416824	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10418100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419111	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10426020	0.88[AMR][1000 genomes]
rs10426049	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10426243	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10500284	0.85[EUR][1000 genomes]
rs12979253	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1811564	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1870093	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2008798	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2008808	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2199829	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2199830	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28821622	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28824227	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28847113	0.85[EUR][1000 genomes]
rs34819714	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795022	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4480913	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62117403	0.85[EUR][1000 genomes]
rs6508998	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6508999	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6509000	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7251154	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7251336	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251783	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251799	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251960	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7258053	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs734107	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs734109	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8099934	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8100182	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8106505	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8110199	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8113283	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113538	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113641	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113720	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113741	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8113813	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs899662	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10419827	DMRTC2	cis	Whole Blood	GTEx
rs10419827	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42298800-42307400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr19:42303000-42307000	Enhancers	Esophagus	oesophagus
3	chr19:42304800-42316800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr19:42305000-42307000	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr19:42305000-42307200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr19:42305000-42309000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:42305000-42310000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr19:42305200-42307000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:42305200-42307000	Enhancers	Fetal Thymus	thymus
10	chr19:42305200-42308800	Enhancers	Primary B cells from peripheral blood	blood
11	chr19:42305600-42307000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:42305600-42308200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:42305800-42307000	Enhancers	Adipose Nuclei	Adipose
14	chr19:42305800-42308200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:42306000-42307200	Enhancers	GM12878-XiMat	blood
16	chr19:42306200-42307000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:42306200-42307200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr19:42306600-42307000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:42306600-42307400	Enhancers	Primary B cells from cord blood	blood

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