Variant report

Variant	rs2905852
Chromosome Location	chr17:46075391-46075392
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46018307..46020101-chr17:46073877..46076464,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234494	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11079804	0.88[CHB][hapmap]
rs11545723	0.94[CHB][hapmap]
rs1476578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476579	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617250	0.88[CHB][hapmap]
rs2003477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003478	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255697	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255815	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2525084	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2525085	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525088	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525091	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525092	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525093	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525094	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525096	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2597161	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597165	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597166	0.90[AFR][1000 genomes]
rs2597168	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597171	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597180	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597181	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905845	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2905846	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905848	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905850	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34190379	0.92[ASN][1000 genomes]
rs35653190	0.85[ASN][1000 genomes]
rs4793734	0.94[CHB][hapmap]
rs4794225	0.82[CHB][hapmap]
rs62064873	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503949	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs739853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7406338	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7503584	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs8076314	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885634	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46061800-46079600	Weak transcription	Right Atrium	heart
2	chr17:46068000-46079800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr17:46069000-46077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:46069000-46079600	Weak transcription	Fetal Thymus	thymus
5	chr17:46073200-46078800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:46073400-46076800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr17:46073400-46077000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:46073400-46077000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:46073400-46081000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:46073800-46077000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:46073800-46077000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:46073800-46077000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46073800-46077000	Weak transcription	Fetal Brain Female	brain
14	chr17:46073800-46078800	Weak transcription	Brain Germinal Matrix	brain
15	chr17:46073800-46079600	Weak transcription	Esophagus	oesophagus
16	chr17:46074000-46077000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:46074000-46077000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:46074200-46075400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr17:46074200-46076400	Weak transcription	Fetal Brain Male	brain
20	chr17:46074200-46077000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr17:46074200-46078800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr17:46074200-46079600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:46074200-46079600	Weak transcription	K562	blood
24	chr17:46074200-46079800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr17:46074400-46077000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:46074600-46075800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr17:46074600-46076000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:46074800-46075400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:46074800-46075600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:46074800-46075600	Enhancers	Fetal Muscle Leg	muscle
31	chr17:46075000-46075600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:46075000-46075600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:46075000-46075800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:46075000-46076000	Enhancers	HSMM	muscle
35	chr17:46075200-46075400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr17:46075200-46075600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:46075200-46075600	Enhancers	Adipose Nuclei	Adipose
38	chr17:46075200-46075600	Enhancers	Placenta	Placenta
39	chr17:46075200-46075600	Flanking Active TSS	HSMMtube	muscle
40	chr17:46075200-46075800	Enhancers	Monocytes-CD14+_RO01746	blood

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