Variant report

Variant	rs6852226
Chromosome Location	chr4:148511272-148511273
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:148440067..148441110-chr4:148510925..148512204,7	MCF-7	breast:
2	chr4:148081448..148083313-chr4:148510559..148512058,10	K562	blood:
3	chr4:148509882..148511690-chr4:148787031..148789794,2	MCF-7	breast:
4	chr4:148031854..148032569-chr4:148511175..148512068,3	MCF-7	breast:
5	chr4:148031852..148032807-chr4:148511183..148512139,6	MCF-7	breast:
6	chr4:148078667..148079597-chr4:148511157..148512035,4	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10006729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10007819	0.82[EUR][1000 genomes]
rs10025254	0.85[EUR][1000 genomes]
rs10028794	0.87[ASN][1000 genomes]
rs10049595	0.83[EUR][1000 genomes]
rs10049817	0.83[EUR][1000 genomes]
rs10434124	0.83[EUR][1000 genomes]
rs10434125	0.83[EUR][1000 genomes]
rs11099659	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099660	0.87[ASN][1000 genomes]
rs11099661	0.84[EUR][1000 genomes]
rs11722231	0.83[EUR][1000 genomes]
rs11723296	0.83[EUR][1000 genomes]
rs11723354	0.83[EUR][1000 genomes]
rs11724387	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11729128	0.83[EUR][1000 genomes]
rs11731451	0.83[EUR][1000 genomes]
rs11732778	0.86[ASN][1000 genomes]
rs11735245	0.85[EUR][1000 genomes]
rs11737524	0.83[EUR][1000 genomes]
rs11945031	0.86[ASN][1000 genomes]
rs12640053	0.85[EUR][1000 genomes]
rs28434099	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28485045	0.83[EUR][1000 genomes]
rs28558982	0.83[EUR][1000 genomes]
rs4835088	0.86[EUR][1000 genomes]
rs4835089	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4835426	0.87[ASN][1000 genomes]
rs4835427	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4835428	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4835430	0.83[EUR][1000 genomes]
rs4835431	0.83[EUR][1000 genomes]
rs4835432	0.83[EUR][1000 genomes]
rs4835433	0.83[EUR][1000 genomes]
rs4835434	0.83[EUR][1000 genomes]
rs4835435	0.83[EUR][1000 genomes]
rs4835436	0.83[EUR][1000 genomes]
rs4835437	0.82[EUR][1000 genomes]
rs6535545	0.85[EUR][1000 genomes]
rs6811966	0.85[EUR][1000 genomes]
rs6816419	0.82[EUR][1000 genomes]
rs6816928	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823363	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6824051	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836543	0.85[EUR][1000 genomes]
rs6841995	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6849644	0.83[EUR][1000 genomes]
rs6849966	0.83[EUR][1000 genomes]
rs6850429	0.83[EUR][1000 genomes]
rs6855155	0.85[EUR][1000 genomes]
rs6855339	0.87[ASN][1000 genomes]
rs6857300	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857312	0.86[EUR][1000 genomes]
rs6857532	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996115	0.82[EUR][1000 genomes]
rs9998608	0.83[EUR][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
rs6852226	TMEM184C	cis	Thyroid	GTEx
rs6852226	PRMT10	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148507200-148511400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:148509400-148511400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr4:148509400-148512400	Enhancers	Hela-S3	cervix
4	chr4:148510200-148512400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:148510200-148520800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:148510400-148511400	Enhancers	Brain Anterior Caudate	brain
7	chr4:148510400-148512000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:148510600-148511400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:148510600-148512400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:148510800-148511600	Enhancers	Osteobl	bone
11	chr4:148510800-148512000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:148510800-148512000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:148510800-148512000	Enhancers	Ovary	ovary
14	chr4:148510800-148512400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr4:148510800-148512600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:148510800-148512600	Enhancers	NHLF	lung
17	chr4:148511000-148511600	Enhancers	Adipose Nuclei	Adipose
18	chr4:148511000-148511600	Enhancers	NH-A	brain
19	chr4:148511200-148511400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:148511200-148511400	Weak transcription	HSMM	muscle
21	chr4:148511200-148512200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr4:148511200-148512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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