Variant report

Variant	rs6828659
Chromosome Location	chr4:165882034-165882035
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:165877542..165879531-chr4:165880684..165882237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250486	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10001548	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016502	0.86[ASN][1000 genomes]
rs10020142	0.89[ASN][1000 genomes]
rs10020204	0.86[ASN][1000 genomes]
rs10025595	0.89[ASN][1000 genomes]
rs10034083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100586	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11936657	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11941364	0.86[ASN][1000 genomes]
rs12501482	0.89[ASN][1000 genomes]
rs12510353	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12510406	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28475532	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28544252	0.81[ASN][1000 genomes]
rs28548593	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28581275	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28624277	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28631315	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28633542	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3196673	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4350966	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4380479	0.89[ASN][1000 genomes]
rs4396952	0.86[ASN][1000 genomes]
rs4511961	0.87[ASN][1000 genomes]
rs56231925	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6536884	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6814756	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6827270	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848637	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680569	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv967697	chr4:165843736-165889668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	esv2760876	chr4:165861386-165893486	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	esv20237	chr4:165861441-165883885	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
16	nsv10607	chr4:165861465-165886549	Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
17	esv2421831	chr4:165868229-165882293	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
18	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
rs6828659	FAM218A	cis	Thyroid	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:165878800-165884000	Weak transcription	Pancreas	Pancrea
2	chr4:165878800-165888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:165878800-165888600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:165878800-165891800	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:165878800-165892000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:165878800-165893400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr4:165878800-165893600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:165878800-165895000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:165878800-165895200	Weak transcription	Fetal Thymus	thymus
10	chr4:165878800-165897800	Weak transcription	Left Ventricle	heart
11	chr4:165878800-165898200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:165879000-165897600	Weak transcription	Fetal Lung	lung
13	chr4:165879000-165897800	Weak transcription	Adipose Nuclei	Adipose
14	chr4:165879200-165893400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:165879200-165894800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:165879400-165892000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:165879400-165897600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:165879400-165898000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:165879600-165882200	Weak transcription	Brain Hippocampus Middle	brain
20	chr4:165879600-165888600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:165879600-165889800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr4:165879600-165893600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:165879800-165898000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:165880000-165888000	Weak transcription	GM12878-XiMat	blood
25	chr4:165880000-165897600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:165880200-165897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:165881200-165882200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:165881200-165883600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:165881400-165897800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:165881600-165882200	Enhancers	HSMM	muscle
31	chr4:165881600-165888600	Weak transcription	Fetal Intestine Large	intestine
32	chr4:165881600-165892000	Weak transcription	Fetal Intestine Small	intestine
33	chr4:165881600-165897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:165881600-165898000	Weak transcription	Osteobl	bone
35	chr4:165882000-165882200	Enhancers	HSMMtube	muscle

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