Variant report

Variant	rs1806086
Chromosome Location	chr5:9197548-9197549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12515855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12519261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17253526	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1806081	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1806082	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1806083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1806085	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1806092	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1806111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1806126	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs183152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs183705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2428652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3822771	0.82[EUR][1000 genomes]
rs3846576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40686	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs40687	1.00[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs40688	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs40689	0.84[LWK][hapmap];0.87[MEX][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs40690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40691	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40695	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40699	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs40717	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62340977	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62340978	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62343369	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6555594	0.93[CEU][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	15 gene(s)	inside rSNPs	diseases
15	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
17	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
19	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1806086	NSUN2	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:9154000-9226200	Weak transcription	Fetal Intestine Large	intestine
3	chr5:9169800-9202800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:9175400-9208400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:9175600-9227400	Weak transcription	Colonic Mucosa	Colon
6	chr5:9185400-9264600	Weak transcription	Left Ventricle	heart
7	chr5:9189400-9228200	Weak transcription	Right Ventricle	heart
8	chr5:9190000-9203400	Weak transcription	Fetal Heart	heart
9	chr5:9190600-9228600	Weak transcription	Esophagus	oesophagus
10	chr5:9191000-9199200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:9192000-9199000	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr5:9192600-9199000	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr5:9192800-9239600	Weak transcription	Pancreas	Pancrea
14	chr5:9194000-9222200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:9195000-9203400	Weak transcription	Fetal Lung	lung
16	chr5:9195200-9208200	Weak transcription	Fetal Kidney	kidney
17	chr5:9195400-9197600	Strong transcription	Fetal Intestine Small	intestine
18	chr5:9195800-9198600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:9196000-9197600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:9196000-9197600	Strong transcription	Fetal Muscle Leg	muscle
21	chr5:9196000-9197600	Strong transcription	Fetal Stomach	stomach
22	chr5:9196000-9197800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:9196000-9197800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:9196000-9198000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:9196000-9198800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:9196000-9199000	Enhancers	NHDF-Ad	bronchial
27	chr5:9196000-9199600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:9196200-9197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:9196200-9197800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:9196200-9197800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr5:9196200-9199000	Enhancers	NH-A	brain
32	chr5:9196200-9202600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:9196400-9197600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:9196400-9198800	Enhancers	NHLF	lung
35	chr5:9196400-9198800	Enhancers	Osteobl	bone
36	chr5:9196600-9197600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:9196600-9198600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:9196600-9198600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:9196600-9198800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:9197000-9197600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:9197000-9197800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:9197000-9197800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:9197000-9202800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr5:9197000-9210000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:9197200-9197600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:9197200-9218800	Weak transcription	Liver	Liver
47	chr5:9197400-9197600	ZNF genes & repeats	Aorta	Aorta
48	chr5:9197400-9197800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr5:9197400-9197800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr5:9197400-9197800	ZNF genes & repeats	GM12878-XiMat	blood

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