Variant report

Variant	rs28475532
Chromosome Location	chr4:165895228-165895229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10001548	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016502	0.86[ASN][1000 genomes]
rs10020142	0.82[ASN][1000 genomes]
rs10020204	0.86[ASN][1000 genomes]
rs10025595	0.82[ASN][1000 genomes]
rs10034083	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100586	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11936657	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11941364	0.86[ASN][1000 genomes]
rs12501482	0.82[ASN][1000 genomes]
rs12510353	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12510406	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28548593	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28581275	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28624277	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28631315	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28633542	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3196673	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4350966	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4380479	0.82[ASN][1000 genomes]
rs4396952	0.86[ASN][1000 genomes]
rs4511961	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56231925	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6536884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6814756	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6827270	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6828659	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848637	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680569	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019150	chr4:165505585-165907924	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1026152	chr4:165622244-166027447	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv537336	chr4:165622244-166027447	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv880382	chr4:165793001-165964290	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	esv2757965	chr4:165801816-165976350	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv2759299	chr4:165801816-165976350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv528686	chr4:165814359-165930168	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1015970	chr4:165852926-165973078	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv830140	chr4:165855999-165956612	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28475532	FAM218A	cis	Thyroid	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165878800-165897800	Weak transcription	Left Ventricle	heart
2	chr4:165878800-165898200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:165879000-165897600	Weak transcription	Fetal Lung	lung
4	chr4:165879000-165897800	Weak transcription	Adipose Nuclei	Adipose
5	chr4:165879400-165897600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:165879400-165898000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:165879800-165898000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:165880000-165897600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:165880200-165897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr4:165881400-165897800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:165881600-165897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:165881600-165898000	Weak transcription	Osteobl	bone
13	chr4:165882200-165897800	Weak transcription	HSMM	muscle
14	chr4:165884600-165898200	Weak transcription	Ovary	ovary
15	chr4:165886800-165897600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:165887000-165898200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:165887200-165898000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:165888800-165895600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:165888800-165895600	Weak transcription	GM12878-XiMat	blood
20	chr4:165888800-165897600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:165888800-165898000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:165889400-165897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:165889800-165897800	Weak transcription	Right Ventricle	heart
24	chr4:165891000-165896200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:165891400-165897600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:165891400-165897800	Weak transcription	Brain Substantia Nigra	brain
27	chr4:165891800-165896400	Strong transcription	Fetal Muscle Leg	muscle
28	chr4:165892000-165895600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:165892000-165895800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:165892000-165896000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:165892000-165896000	Strong transcription	Fetal Intestine Small	intestine
32	chr4:165892000-165896600	Strong transcription	Fetal Stomach	stomach
33	chr4:165892200-165897600	Weak transcription	NHDF-Ad	bronchial
34	chr4:165892200-165898200	Weak transcription	Lung	lung
35	chr4:165892400-165896000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:165892800-165897600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:165893400-165895400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr4:165893400-165896000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:165893400-165896200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:165893400-165896600	Strong transcription	Fetal Intestine Large	intestine
41	chr4:165893600-165896000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:165894000-165898000	Weak transcription	Fetal Brain Female	brain
43	chr4:165894400-165898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr4:165894600-165895600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:165894800-165898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:165895000-165896400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:165895000-165897800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:165895000-165898200	Weak transcription	Brain Germinal Matrix	brain
49	chr4:165895200-165896000	Strong transcription	Fetal Thymus	thymus
50	chr4:165895200-165897200	Strong transcription	Fetal Muscle Trunk	muscle

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