Variant report

Variant	rs268486
Chromosome Location	chr5:9426734-9426735
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10068683	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11951666	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs16882704	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16882748	0.88[TSI][hapmap]
rs268479	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap]
rs268480	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs268481	1.00[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs268536	0.86[EUR][1000 genomes]
rs3846587	0.83[LWK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs414293	0.93[CEU][hapmap]
rs666617	0.87[CEU][hapmap]
rs6873574	0.89[YRI][hapmap]
rs7709896	0.99[EUR][1000 genomes]
rs979581	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv597072	chr5:9423834-9438566	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs268486	NSUN2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9379000-9434800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:9379000-9436200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:9380200-9429800	Weak transcription	Ovary	ovary
4	chr5:9395800-9450200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:9398600-9435600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:9411000-9430400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:9411800-9426800	Weak transcription	Fetal Intestine Large	intestine
8	chr5:9417800-9438600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:9419400-9430000	Weak transcription	Colonic Mucosa	Colon
10	chr5:9419600-9431600	Weak transcription	Pancreas	Pancrea
11	chr5:9419800-9430600	Weak transcription	Esophagus	oesophagus
12	chr5:9420400-9429600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:9420400-9429800	Weak transcription	Fetal Stomach	stomach
14	chr5:9420600-9430000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:9421000-9429800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:9421400-9431600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:9422400-9431400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:9422800-9437000	Weak transcription	Aorta	Aorta
19	chr5:9423400-9431800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr5:9423800-9430600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:9423800-9431400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:9424000-9427200	Weak transcription	Left Ventricle	heart
23	chr5:9424000-9431400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:9424200-9430600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:9424400-9426800	Weak transcription	NHLF	lung
26	chr5:9424800-9430200	Weak transcription	NHDF-Ad	bronchial
27	chr5:9425000-9430600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:9425200-9429200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:9425200-9430600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:9425200-9431600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:9425800-9427000	Weak transcription	Fetal Kidney	kidney
32	chr5:9425800-9427200	Weak transcription	Fetal Lung	lung
33	chr5:9425800-9430200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:9426000-9430800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:9426200-9427400	Weak transcription	Fetal Heart	heart
36	chr5:9426400-9428400	Weak transcription	Right Ventricle	heart
37	chr5:9426600-9427800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr5:9426600-9427800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:9426600-9429200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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