Variant report

Variant	rs4798489
Chromosome Location	chr18:6755698-6755699
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10853339	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081256	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11081258	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11081261	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081262	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081263	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081265	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663818	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11663883	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11876610	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12456109	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12458536	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12458555	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12605298	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12956941	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12962460	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13381520	0.85[EUR][1000 genomes]
rs28402892	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28675797	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34146208	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35451382	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4078265	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4605246	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4798486	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4798490	0.84[ASN][1000 genomes]
rs55847427	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57509765	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6417043	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506429	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506430	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506431	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506432	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506434	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506438	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6506439	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7227965	0.87[EUR][1000 genomes]
rs7228459	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7232028	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7232807	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7233049	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7233410	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7233739	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7235385	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7237087	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7237204	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7238175	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7239808	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7242667	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7504466	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7505283	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7506354	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7506610	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7506974	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8084747	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8088863	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8093374	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9952482	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059678	chr18:6155114-6838290	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv916883	chr18:6299209-7244642	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS 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	42 gene(s)	inside rSNPs	diseases
3	nsv1055148	chr18:6527292-6790869	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv543629	chr18:6527292-6790869	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3529901	chr18:6537233-6851509	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3529902	chr18:6537233-6851509	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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
7	nsv1063762	chr18:6542534-7382339	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv543630	chr18:6542534-7382339	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription 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 target site	39 gene(s)	inside rSNPs	diseases
9	nsv1060757	chr18:6682974-7051982	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv543631	chr18:6682974-7051982	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv1064175	chr18:6740267-7384528	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	esv34611	chr18:6741970-6838290	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4798489	RP11-91I8.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6736000-6761400	Weak transcription	Spleen	Spleen
2	chr18:6741600-6761400	Weak transcription	Pancreas	Pancrea
3	chr18:6749000-6756600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr18:6749000-6757800	Weak transcription	Fetal Heart	heart
5	chr18:6750800-6757800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:6751200-6756600	Weak transcription	Psoas Muscle	Psoas
7	chr18:6751800-6757800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:6751800-6758200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr18:6752400-6759600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr18:6752400-6761000	Weak transcription	Placenta	Placenta
11	chr18:6752600-6756400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr18:6752600-6757800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr18:6752800-6756600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr18:6752800-6757800	Weak transcription	Adipose Nuclei	Adipose
15	chr18:6752800-6757800	Weak transcription	Fetal Muscle Leg	muscle
16	chr18:6752800-6757800	Weak transcription	Ovary	ovary
17	chr18:6752800-6773800	Weak transcription	Right Atrium	heart
18	chr18:6753000-6756800	Enhancers	Fetal Lung	lung
19	chr18:6753000-6757800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr18:6753200-6756200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr18:6753200-6757200	Weak transcription	HSMM	muscle
22	chr18:6753200-6757600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr18:6753200-6757600	Weak transcription	HSMMtube	muscle
24	chr18:6753200-6757600	Weak transcription	NH-A	brain
25	chr18:6753200-6758000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr18:6753200-6758200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr18:6753200-6759800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr18:6753200-6763600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr18:6753400-6757400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:6753800-6758000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr18:6754000-6756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr18:6754000-6757400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr18:6754000-6757600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr18:6754400-6755800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr18:6754400-6756000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr18:6754400-6756600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:6754800-6756000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr18:6754800-6756200	Enhancers	HUVEC	blood vessel
39	chr18:6755200-6755800	Enhancers	NHDF-Ad	bronchial
40	chr18:6755200-6761400	Weak transcription	Lung	lung
41	chr18:6755400-6756800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr18:6755600-6756000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:6755600-6757600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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