Variant report

Variant	rs16871694
Chromosome Location	chr6:44244970-44244971
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1044690	0.90[CEU][hapmap]
rs1056092	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1056093	0.81[MEX][hapmap]
rs3175074	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55868013	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6900895	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7451189	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7772266	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9472246	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv603003	chr6:44191920-44253765	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv524398	chr6:44200953-44253765	Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
7	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
8	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
9	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv885857	chr6:44223010-44250165	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
11	esv3422155	chr6:44242599-44245147	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16871694	CDC5L	cis	parietal	SCAN
rs16871694	C6orf223	cis	cerebellum	SCAN
rs16871694	TCTE1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44239600-44247600	Enhancers	Fetal Brain Male	brain
2	chr6:44240800-44245000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:44241200-44252200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:44242400-44245200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:44243600-44246600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:44243800-44245600	Strong transcription	Fetal Brain Female	brain
7	chr6:44244000-44247000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:44244200-44245000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:44244200-44245000	Genic enhancers	Brain Germinal Matrix	brain
10	chr6:44244200-44245000	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr6:44244200-44247800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:44244200-44250600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:44244400-44251000	Weak transcription	Gastric	stomach
14	chr6:44244400-44257400	Weak transcription	Pancreas	Pancrea
15	chr6:44244400-44264800	Weak transcription	Right Atrium	heart
16	chr6:44244600-44245200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:44244800-44245000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
18	chr6:44244800-44248000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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