Variant report

Variant	rs4129805
Chromosome Location	chr2:100586506-100586507
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	chr2:100577188..100580714-chr2:100582263..100586787,5	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10165066	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs10183465	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10187195	0.99[EUR][1000 genomes]
rs10189707	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10198187	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10209198	0.87[EUR][1000 genomes]
rs10211423	1.00[MEX][hapmap]
rs11887136	0.98[EUR][1000 genomes]
rs11897706	0.95[EUR][1000 genomes]
rs13382597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13383014	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13385193	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13393937	0.84[EUR][1000 genomes]
rs13405987	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13410695	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13410884	0.98[EUR][1000 genomes]
rs13413309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13416574	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1574207	0.87[EUR][1000 genomes]
rs17023362	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17023378	0.88[EUR][1000 genomes]
rs17023391	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17023393	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17436955	0.89[EUR][1000 genomes]
rs2001722	0.87[EUR][1000 genomes]
rs2309775	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4449188	0.83[EUR][1000 genomes]
rs4641993	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55649403	0.85[EUR][1000 genomes]
rs55681051	0.85[EUR][1000 genomes]
rs56332326	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs57360658	0.96[EUR][1000 genomes]
rs58270548	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62147652	0.85[EUR][1000 genomes]
rs62147658	0.85[EUR][1000 genomes]
rs62147659	0.87[EUR][1000 genomes]
rs62149260	0.87[EUR][1000 genomes]
rs62149262	0.87[EUR][1000 genomes]
rs62149263	0.87[EUR][1000 genomes]
rs62149264	0.81[EUR][1000 genomes]
rs62149268	0.87[EUR][1000 genomes]
rs62149270	0.88[EUR][1000 genomes]
rs62149271	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62149272	0.88[EUR][1000 genomes]
rs62149296	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62149297	0.88[EUR][1000 genomes]
rs62149298	0.89[EUR][1000 genomes]
rs62149299	0.89[EUR][1000 genomes]
rs62149301	0.89[EUR][1000 genomes]
rs62149302	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6736239	0.85[EUR][1000 genomes]
rs72819146	0.85[EUR][1000 genomes]
rs72819147	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72819148	0.87[EUR][1000 genomes]
rs72819149	0.87[EUR][1000 genomes]
rs72819157	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72819165	0.85[EUR][1000 genomes]
rs7425132	0.96[EUR][1000 genomes]
rs7573669	0.85[EUR][1000 genomes]
rs7576469	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7577040	0.96[EUR][1000 genomes]
rs9308831	0.89[EUR][1000 genomes]
rs9308832	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1003114	chr2:100480432-100601586	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129805	RPL31	cis	cerebellum	SCAN
rs4129805	AFF3	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100550800-100618200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:100563200-100625400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:100564800-100617000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:100570600-100598400	Weak transcription	Dnd41	blood
5	chr2:100573800-100599600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:100574400-100591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:100577200-100590800	Weak transcription	Fetal Kidney	kidney
8	chr2:100577400-100618200	Weak transcription	Aorta	Aorta
9	chr2:100577600-100587000	Weak transcription	Lung	lung
10	chr2:100577800-100603400	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:100577800-100607400	Weak transcription	Thymus	Thymus
12	chr2:100577800-100623000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:100577800-100623000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:100578000-100589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:100578000-100616200	Weak transcription	Fetal Thymus	thymus
16	chr2:100578400-100589000	Weak transcription	Fetal Brain Female	brain
17	chr2:100578400-100591000	Weak transcription	Fetal Brain Male	brain
18	chr2:100578800-100588800	Weak transcription	Fetal Lung	lung
19	chr2:100578800-100589200	Weak transcription	Gastric	stomach
20	chr2:100582400-100608000	Weak transcription	Fetal Stomach	stomach
21	chr2:100583200-100608000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr2:100585800-100587000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:100585800-100588800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:100585800-100594000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:100586000-100586800	Weak transcription	Primary B cells from cord blood	blood
26	chr2:100586000-100598200	Weak transcription	Primary T cells from cord blood	blood
27	chr2:100586200-100586600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:100586400-100586800	Enhancers	Osteobl	bone
29	chr2:100586400-100587200	Enhancers	Liver	Liver
30	chr2:100586400-100587200	Enhancers	NHLF	lung

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