Variant report

Variant	rs28558982
Chromosome Location	chr4:148518437-148518438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10006729	0.83[EUR][1000 genomes]
rs10007819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10021513	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10025254	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10049595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10049817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10434125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099657	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11099658	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11099659	0.84[EUR][1000 genomes]
rs11099661	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11722231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723296	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11729128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11735245	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737524	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929879	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12640053	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28434099	0.80[EUR][1000 genomes]
rs28485045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835088	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835089	0.83[EUR][1000 genomes]
rs4835427	0.82[EUR][1000 genomes]
rs4835428	0.83[EUR][1000 genomes]
rs4835430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535545	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811966	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816419	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816928	0.84[EUR][1000 genomes]
rs6824051	0.84[EUR][1000 genomes]
rs6836543	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841995	0.84[EUR][1000 genomes]
rs6849644	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849966	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850429	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6852226	0.83[EUR][1000 genomes]
rs6855155	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857300	0.83[EUR][1000 genomes]
rs6857312	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857532	0.82[EUR][1000 genomes]
rs7675774	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7695363	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9996115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9998608	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830110	chr4:148432125-148595119	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv428776	chr4:148432125-148595119	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	esv13564	chr4:148515649-148519825	Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	nsv595653	chr4:148515669-148519339	Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv595654	chr4:148515669-148519535	Enhancers Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
7	esv1840088	chr4:148515669-148519763	Enhancers Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	esv1829169	chr4:148515833-148519535	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
9	esv1832941	chr4:148515833-148519535	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
10	esv1845878	chr4:148515833-148519535	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
11	esv1849976	chr4:148515833-148519535	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
12	esv2763396	chr4:148516769-148535636	Enhancers Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv595655	chr4:148518245-148519763	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28558982	TMEM184C	cis	Thyroid	GTEx
rs28558982	PRMT10	cis	Thyroid	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148510200-148520800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:148517600-148518600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:148517800-148518600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:148517800-148518600	Enhancers	NHEK	skin
5	chr4:148517800-148518800	Enhancers	HMEC	breast
6	chr4:148517800-148519000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:148518000-148518600	Enhancers	HSMMtube	muscle
8	chr4:148518000-148518800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:148518000-148518800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:148518000-148518800	Enhancers	Pancreas	Pancrea
11	chr4:148518000-148518800	Enhancers	HSMM	muscle
12	chr4:148518000-148518800	Enhancers	HUVEC	blood vessel
13	chr4:148518000-148519000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:148518000-148519000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:148518000-148519000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:148518000-148519000	Enhancers	NHDF-Ad	bronchial
17	chr4:148518000-148519200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:148518000-148519200	Enhancers	NH-A	brain
19	chr4:148518000-148519200	Enhancers	NHLF	lung
20	chr4:148518000-148519200	Enhancers	Osteobl	bone
21	chr4:148518000-148519400	Enhancers	Hela-S3	cervix
22	chr4:148518000-148519800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:148518200-148518600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:148518200-148518600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:148518200-148518600	Enhancers	Stomach Mucosa	stomach
26	chr4:148518200-148518800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:148518200-148519000	Enhancers	Stomach Smooth Muscle	stomach
28	chr4:148518400-148518800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:148518400-148519200	Enhancers	Aorta	Aorta
30	chr4:148518400-148520800	Weak transcription	A549	lung

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