Variant report

Variant	rs6857999
Chromosome Location	chr4:47515189-47515190
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs4132384	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4423850	0.97[EUR][1000 genomes]
rs4467534	0.97[EUR][1000 genomes]
rs4467535	0.97[EUR][1000 genomes]
rs4475121	0.99[EUR][1000 genomes]
rs4694851	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs4695239	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4695243	1.00[CHD][hapmap]
rs6447564	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6842769	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6849863	0.99[EUR][1000 genomes]
rs73237070	0.97[EUR][1000 genomes]
rs73237074	0.98[EUR][1000 genomes]
rs73237078	0.99[EUR][1000 genomes]
rs73237080	0.99[EUR][1000 genomes]
rs73237082	0.99[EUR][1000 genomes]
rs73237084	0.97[EUR][1000 genomes]
rs73237085	0.97[EUR][1000 genomes]
rs73237086	0.96[EUR][1000 genomes]
rs73237087	0.92[EUR][1000 genomes]
rs73237088	0.92[EUR][1000 genomes]
rs73237089	0.92[EUR][1000 genomes]
rs73237091	0.90[EUR][1000 genomes]
rs7662844	1.00[ASN][1000 genomes]
rs7674353	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7675970	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879005	chr4:47408838-47548254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv829923	chr4:47436139-47678443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6857999	CNGA1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47488000-47533800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:47488600-47524600	Weak transcription	Fetal Intestine Small	intestine
3	chr4:47488800-47559800	Weak transcription	Right Ventricle	heart
4	chr4:47489200-47533600	Weak transcription	Esophagus	oesophagus
5	chr4:47501000-47527600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:47502200-47533000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr4:47503200-47521200	Weak transcription	Spleen	Spleen
8	chr4:47507600-47515600	Weak transcription	NHLF	lung
9	chr4:47507800-47515400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:47507800-47526400	Weak transcription	NHDF-Ad	bronchial
11	chr4:47507800-47527800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:47510000-47526000	Weak transcription	Pancreas	Pancrea
13	chr4:47512200-47536800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:47512400-47515400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:47512400-47530200	Weak transcription	Fetal Brain Male	brain
16	chr4:47512400-47577200	Weak transcription	Small Intestine	intestine
17	chr4:47512600-47515600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:47512800-47515200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:47512800-47515400	Weak transcription	Adipose Nuclei	Adipose
20	chr4:47512800-47517200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:47512800-47517800	Weak transcription	Brain Angular Gyrus	brain
22	chr4:47512800-47532600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:47513000-47515400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:47513000-47527600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:47513200-47521200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:47513200-47521200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:47513400-47515600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:47513400-47521400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:47513600-47515200	Weak transcription	Fetal Intestine Large	intestine
30	chr4:47513600-47515200	Weak transcription	Stomach Mucosa	stomach
31	chr4:47513600-47515400	Weak transcription	Primary T cells from cord blood	blood
32	chr4:47513600-47515600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:47513600-47533200	Weak transcription	Brain Substantia Nigra	brain
34	chr4:47513800-47530600	Weak transcription	Fetal Heart	heart
35	chr4:47513800-47534000	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:47514000-47515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:47514000-47517200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:47514000-47524200	Weak transcription	Liver	Liver
39	chr4:47514000-47531400	Weak transcription	Brain Anterior Caudate	brain
40	chr4:47514000-47551000	Weak transcription	Gastric	stomach
41	chr4:47514200-47515200	Weak transcription	HUVEC	blood vessel
42	chr4:47514200-47515600	Weak transcription	NHEK	skin
43	chr4:47514200-47518000	Strong transcription	NH-A	brain
44	chr4:47514200-47519000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:47514200-47533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:47514400-47515400	Strong transcription	Fetal Stomach	stomach
47	chr4:47514400-47515800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:47514400-47515800	Strong transcription	Lung	lung
49	chr4:47514400-47515800	Genic enhancers	Dnd41	blood
50	chr4:47514400-47516200	Strong transcription	Fetal Lung	lung

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