Variant report

Variant	rs4476827
Chromosome Location	chr6:53676187-53676188
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53657579..53660733-chr6:53674241..53678049,6	MCF-7	breast:
2	chr6:53588027..53590620-chr6:53675669..53678421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10498795	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543356	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs16884427	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17748452	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2223617	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2473603	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2820217	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs2820218	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3000998	0.85[CHB][hapmap]
rs3799261	1.00[JPT][hapmap]
rs4077760	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4131378	0.86[EUR][1000 genomes]
rs4272222	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4276504	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4357137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4380749	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397225	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580851	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908101	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6919924	0.88[EUR][1000 genomes]
rs6925165	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761135	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs7752696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474672	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4476827	COL21A1	cis	cerebellum	SCAN
rs4476827	C6orf142	cis	cerebellum	SCAN
rs4476827	FBXO9	cis	parietal	SCAN
rs4476827	LRRC1	cis	parietal	SCAN
rs4476827	TFAP2D	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
3	chr6:53667600-53678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
5	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:53668800-53683800	Weak transcription	Ovary	ovary
7	chr6:53669800-53676800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:53670200-53678000	Weak transcription	Aorta	Aorta
9	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:53671000-53676400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
16	chr6:53671400-53676400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:53671400-53679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:53671600-53676200	Weak transcription	Gastric	stomach
19	chr6:53673000-53678400	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:53673600-53677800	Weak transcription	Brain Substantia Nigra	brain
22	chr6:53673600-53682800	Weak transcription	Dnd41	blood
23	chr6:53673800-53678600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:53674200-53678200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:53674600-53677200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:53674800-53678400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:53674800-53679600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
29	chr6:53675000-53676200	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:53675000-53676400	Enhancers	Brain Germinal Matrix	brain
31	chr6:53675000-53676600	Enhancers	HepG2	liver
32	chr6:53675000-53677000	Enhancers	HMEC	breast
33	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
34	chr6:53675400-53677000	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr6:53675400-53679000	Enhancers	Duodenum Mucosa	Duodenum
36	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
37	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:53675600-53676200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:53675600-53676200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:53675600-53676200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:53675600-53676200	Enhancers	Primary T cells from cord blood	blood
42	chr6:53675600-53676200	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr6:53675600-53676200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:53675600-53676200	Enhancers	Left Ventricle	heart
45	chr6:53675600-53676200	Enhancers	Lung	lung
46	chr6:53675600-53676400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:53675600-53676400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:53675600-53676400	Enhancers	Brain Angular Gyrus	brain
49	chr6:53675600-53676400	Enhancers	Colonic Mucosa	Colon
50	chr6:53675600-53676400	Enhancers	A549	lung

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