Variant report

Variant	rs283055
Chromosome Location	chr6:118645919-118645920
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	chr6:118631014..118632814-chr6:118644282..118647263,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1006932	0.92[ASN][1000 genomes]
rs17079862	0.84[CHB][hapmap]
rs172212	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs176014	0.85[CHB][hapmap]
rs1874082	0.88[AMR][1000 genomes]
rs190756	0.90[CHB][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1923282	0.89[CHB][hapmap]
rs205955	0.87[YRI][hapmap]
rs2501470	0.81[ASN][1000 genomes]
rs281866	0.90[CHB][hapmap]
rs281869	0.90[ASW][hapmap];0.90[CHB][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs281872	0.90[CHB][hapmap]
rs283040	0.80[JPT][hapmap]
rs283047	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs283051	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs283052	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs283053	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs283054	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs283061	0.89[AMR][1000 genomes]
rs283067	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs283083	0.85[CHB][hapmap]
rs2883849	0.90[CHB][hapmap]
rs387266	0.89[AMR][1000 genomes]
rs413876	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs427027	0.83[CHB][hapmap]
rs450093	0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes]
rs4945618	0.85[CHB][hapmap]
rs9320646	0.90[CHB][hapmap]
rs9385038	0.90[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv604554	chr6:118631282-118716318	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv830787	chr6:118631902-118805106	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs283055	NT5DC1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118635400-118646400	Weak transcription	Right Ventricle	heart
2	chr6:118637400-118646400	Weak transcription	Left Ventricle	heart
3	chr6:118641400-118646400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:118641400-118647800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:118641400-118648400	Weak transcription	Psoas Muscle	Psoas
6	chr6:118641800-118646600	Weak transcription	Right Atrium	heart
7	chr6:118642200-118646600	Weak transcription	NHLF	lung
8	chr6:118643200-118646400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:118643400-118646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:118644800-118646000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr6:118644800-118647200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:118644800-118649000	Enhancers	Aorta	Aorta
13	chr6:118645000-118647200	Enhancers	Fetal Heart	heart
14	chr6:118645400-118646000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:118645400-118648400	Enhancers	Stomach Smooth Muscle	stomach
16	chr6:118645400-118649000	Enhancers	Colon Smooth Muscle	Colon
17	chr6:118645600-118646200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:118645800-118646600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:118645800-118646600	Weak transcription	Rectal Smooth Muscle	rectum

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