Variant report

Variant	rs9955885
Chromosome Location	chr18:7661058-7661059
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10153440	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11877002	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1446080	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1664983	0.90[CEU][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16952257	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16952260	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1940347	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1941136	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2032176	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2032177	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28470267	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28750977	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28788217	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55750787	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6506520	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6506523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6506524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6650627	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6650628	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7228736	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7232258	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9946325	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956880	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9961570	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9961754	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[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	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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
7	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9955885	SNORD116-29	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7631000-7662800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr18:7646600-7663200	Weak transcription	Pancreas	Pancrea
3	chr18:7649400-7663000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr18:7656400-7662000	Enhancers	Psoas Muscle	Psoas
5	chr18:7657000-7668400	Weak transcription	Gastric	stomach
6	chr18:7657400-7663000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr18:7657400-7663000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr18:7657400-7664000	Weak transcription	Lung	lung
9	chr18:7657400-7680600	Weak transcription	Ovary	ovary
10	chr18:7657600-7663000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr18:7657800-7664200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:7657800-7668400	Weak transcription	Spleen	Spleen
13	chr18:7657800-7669200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr18:7658000-7669200	Weak transcription	Fetal Stomach	stomach
15	chr18:7658200-7663000	Weak transcription	Fetal Lung	lung
16	chr18:7658800-7661200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr18:7658800-7661400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr18:7658800-7663000	Weak transcription	Brain Anterior Caudate	brain
19	chr18:7659000-7661200	Weak transcription	Aorta	Aorta
20	chr18:7659000-7663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:7659000-7668200	Weak transcription	A549	lung
22	chr18:7659400-7663200	Weak transcription	Fetal Heart	heart
23	chr18:7659600-7663000	Weak transcription	Right Atrium	heart
24	chr18:7659600-7663000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr18:7659600-7668200	Weak transcription	HepG2	liver
26	chr18:7659800-7663000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr18:7660000-7661600	Enhancers	Left Ventricle	heart
28	chr18:7660200-7663000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr18:7660800-7661600	Enhancers	Fetal Muscle Leg	muscle
30	chr18:7660800-7663000	Weak transcription	Right Ventricle	heart
31	chr18:7661000-7664200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr18:7661000-7664200	Enhancers	Adipose Nuclei	Adipose

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