Variant report

Variant	rs4835088
Chromosome Location	chr4:148509519-148509520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10006729	0.86[EUR][1000 genomes]
rs10007819	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10021513	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10025254	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10049595	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10049817	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10434124	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10434125	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11099657	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11099658	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11099659	0.85[EUR][1000 genomes]
rs11099661	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11722231	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11723296	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11723354	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729128	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11731451	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11735245	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737524	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929879	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12640053	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28434099	0.82[EUR][1000 genomes]
rs28485045	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28558982	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835089	0.86[EUR][1000 genomes]
rs4835427	0.85[EUR][1000 genomes]
rs4835428	0.86[EUR][1000 genomes]
rs4835430	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835431	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835432	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835433	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835434	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835435	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835436	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835437	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535545	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811966	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816419	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816928	0.85[EUR][1000 genomes]
rs6824051	0.85[EUR][1000 genomes]
rs6836543	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841995	0.85[EUR][1000 genomes]
rs6849644	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849966	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6850429	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6852226	0.86[EUR][1000 genomes]
rs6855155	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857300	0.86[EUR][1000 genomes]
rs6857312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857532	0.85[EUR][1000 genomes]
rs7675774	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7695363	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9996115	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9998608	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4835088	PRMT10	cis	Thyroid	GTEx
rs4835088	TMEM184C	cis	Thyroid	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148500000-148510800	Weak transcription	Ovary	ovary
2	chr4:148503600-148510800	Weak transcription	HSMM	muscle
3	chr4:148503600-148510800	Weak transcription	Osteobl	bone
4	chr4:148503800-148510800	Weak transcription	HSMMtube	muscle
5	chr4:148506600-148510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:148507200-148511400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:148507400-148510400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:148507400-148510800	Weak transcription	Fetal Stomach	stomach
9	chr4:148507600-148510800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:148508600-148510600	Weak transcription	NHDF-Ad	bronchial
11	chr4:148508600-148510800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr4:148508600-148510800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:148508800-148510600	Weak transcription	Fetal Lung	lung
14	chr4:148508800-148510800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:148508800-148510800	Weak transcription	NHLF	lung
16	chr4:148509000-148510400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:148509000-148510400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:148509200-148510400	Weak transcription	Brain Anterior Caudate	brain
19	chr4:148509200-148510400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:148509200-148510400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:148509200-148510600	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:148509400-148511000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:148509400-148511400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:148509400-148512400	Enhancers	Hela-S3	cervix

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