Variant report

Variant	rs55866900
Chromosome Location	chr18:6741564-6741565
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:6731530..6734164-chr18:6740298..6742070,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11081264	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11660237	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11661838	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11663135	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11663719	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150787	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12326891	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12455302	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13381520	0.81[ASN][1000 genomes]
rs13381524	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4078165	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4797256	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4798487	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56061391	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62081458	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237200	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7505315	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7505383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505419	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	nsv1057885	chr18:6598684-6754548	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55866900	RP11-91I8.3	cis	Muscle Skeletal	GTEx
rs55866900	ARHGAP28	cis	Thyroid	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6730200-6747800	Weak transcription	Left Ventricle	heart
2	chr18:6731800-6743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:6735000-6743800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:6736000-6745600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:6736000-6761400	Weak transcription	Spleen	Spleen
6	chr18:6738800-6743000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr18:6739200-6747600	Weak transcription	Fetal Heart	heart
8	chr18:6740000-6741600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr18:6740000-6743000	Enhancers	NHDF-Ad	bronchial
10	chr18:6740200-6741800	Enhancers	NH-A	brain
11	chr18:6740200-6742200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr18:6740200-6742600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr18:6740200-6742600	Enhancers	NHLF	lung
14	chr18:6740200-6742800	Enhancers	HUVEC	blood vessel
15	chr18:6740200-6743200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr18:6740200-6743200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr18:6740200-6743400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr18:6740400-6741600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr18:6740400-6741600	Enhancers	Psoas Muscle	Psoas
20	chr18:6740400-6741800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr18:6740400-6742200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:6740600-6741600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr18:6740600-6741800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr18:6740600-6742000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr18:6740600-6742200	Enhancers	Fetal Stomach	stomach
26	chr18:6740600-6742200	Enhancers	HMEC	breast
27	chr18:6740800-6741600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:6740800-6741600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr18:6740800-6741600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr18:6740800-6741600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr18:6740800-6741600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr18:6740800-6741600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr18:6740800-6741600	Enhancers	Pancreas	Pancrea
34	chr18:6740800-6741800	Enhancers	Adipose Nuclei	Adipose
35	chr18:6740800-6742000	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr18:6740800-6742000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:6740800-6742000	Enhancers	Colon Smooth Muscle	Colon
38	chr18:6740800-6742200	Enhancers	Hela-S3	cervix
39	chr18:6740800-6743000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr18:6740800-6744400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr18:6741000-6741600	Flanking Active TSS	Fetal Lung	lung
42	chr18:6741000-6741800	Enhancers	K562	blood
43	chr18:6741000-6742200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr18:6741000-6742200	Weak transcription	Ovary	ovary
45	chr18:6741000-6743000	Enhancers	Fetal Muscle Leg	muscle
46	chr18:6741000-6743000	Enhancers	HSMM	muscle
47	chr18:6741000-6747200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr18:6741000-6751200	Weak transcription	Placenta	Placenta
49	chr18:6741200-6742400	Enhancers	Osteobl	bone
50	chr18:6741200-6751600	Weak transcription	H1 Cell Line	embryonic stem cell

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