Variant report

Variant	rs484842
Chromosome Location	chr6:165759915-165759916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:165746371..165749114-chr6:165759117..165761315,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs3778248	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3799146	0.82[ASN][1000 genomes]
rs3799148	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3799156	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3799160	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs471607	0.99[ASN][1000 genomes]
rs472328	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs509939	0.86[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513240	0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs525643	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs537131	0.85[EUR][1000 genomes]
rs541938	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs546221	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs546311	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs550868	0.99[ASN][1000 genomes]
rs551444	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55694649	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs56854061	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs571047	0.87[EUR][1000 genomes]
rs575424	0.84[CHB][hapmap]
rs62442142	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62442144	0.90[ASN][1000 genomes]
rs851951	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs851963	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432982	chr6:165528589-165835589	Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv605245	chr6:165542686-165845903	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1031648	chr6:165544569-165841029	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv432983	chr6:165554403-165851585	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3417270	chr6:165682773-166023032	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv508438	chr6:165703355-165760649	Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv886928	chr6:165722345-166197889	Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs484842	DNTTIP1	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165740400-165760800	Weak transcription	Fetal Kidney	kidney
2	chr6:165744000-165769000	Weak transcription	Ovary	ovary
3	chr6:165744800-165763600	Weak transcription	Brain Anterior Caudate	brain
4	chr6:165744800-165801200	Weak transcription	Hela-S3	cervix
5	chr6:165745200-165770000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:165745400-165763000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:165745600-165802800	Weak transcription	Fetal Heart	heart
8	chr6:165747400-165763000	Weak transcription	Fetal Brain Female	brain
9	chr6:165747400-165802600	Weak transcription	HSMMtube	muscle
10	chr6:165747600-165763200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:165747600-165853000	Weak transcription	A549	lung
12	chr6:165747800-165760800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:165749200-165769800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:165749600-165762600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:165749600-165763200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:165749600-165763200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:165749600-165763400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:165749800-165762400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:165749800-165762800	Weak transcription	Right Ventricle	heart
20	chr6:165749800-165763200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:165749800-165763200	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:165749800-165763200	Weak transcription	Fetal Stomach	stomach
23	chr6:165749800-165775000	Weak transcription	Fetal Lung	lung
24	chr6:165754400-165762600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:165754400-165763200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:165754600-165764800	Weak transcription	Fetal Brain Male	brain
27	chr6:165754800-165763000	Weak transcription	Brain Germinal Matrix	brain
28	chr6:165755200-165760200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:165755400-165761800	Weak transcription	Left Ventricle	heart
30	chr6:165758200-165761800	Weak transcription	Pancreas	Pancrea
31	chr6:165758400-165763200	Weak transcription	HSMM	muscle
32	chr6:165759200-165760000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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