Variant report

Variant	rs551444
Chromosome Location	chr6:165742365-165742366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SDIM1-2	chr6:165740975-165742467	NONHSAT116002

Extended variants
information (count: 32 )
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];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799146	0.82[ASN][1000 genomes]
rs3799148	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3799156	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3799160	0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs471607	0.95[ASN][1000 genomes]
rs472328	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs484842	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]
rs509939	0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs513240	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs525643	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537131	0.86[EUR][1000 genomes]
rs541938	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs546221	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs546311	0.87[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550868	0.95[ASN][1000 genomes]
rs55694649	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56854061	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs571047	0.88[EUR][1000 genomes]
rs575424	0.84[CHB][hapmap]
rs62442142	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62442144	0.88[ASN][1000 genomes]
rs851951	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs851963	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv5586	chr6:165694448-165747217	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	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
8	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
rs551444	DNTTIP1	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165735600-165746200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:165736000-165746400	Weak transcription	HSMMtube	muscle
3	chr6:165738200-165743200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:165738200-165746200	Weak transcription	Left Ventricle	heart
5	chr6:165740400-165746400	Weak transcription	Right Ventricle	heart
6	chr6:165740400-165754200	Weak transcription	Fetal Brain Male	brain
7	chr6:165740400-165760800	Weak transcription	Fetal Kidney	kidney
8	chr6:165740600-165749000	Weak transcription	Placenta	Placenta
9	chr6:165741400-165743400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:165741400-165743400	Strong transcription	HSMM	muscle
11	chr6:165741600-165754000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:165741800-165748800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links