Variant report

Variant	rs6551287
Chromosome Location	chr3:88221933-88221934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88198254..88200113-chr3:88221205..88223839,2	MCF-7	breast:
2	chr3:88220438..88221953-chr3:88224348..88225865,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1006896	0.87[ASN][1000 genomes]
rs10858	0.87[ASN][1000 genomes]
rs11925988	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317202	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735556	0.87[ASN][1000 genomes]
rs2735559	0.87[ASN][1000 genomes]
rs4858934	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858939	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858940	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859003	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883959	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55928667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211058	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246133	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419868	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419869	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551281	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551295	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73132512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132546	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146085	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146095	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146099	0.87[ASN][1000 genomes]
rs73148006	0.80[ASN][1000 genomes]
rs7430022	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610494	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620576	0.91[EUR][1000 genomes]
rs7624215	0.93[EUR][1000 genomes]
rs7650068	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284814	0.90[EUR][1000 genomes]
rs9826925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	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
rs6551287	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
2	chr3:88205600-88222000	Weak transcription	Fetal Stomach	stomach
3	chr3:88205600-88222800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:88205800-88227000	Weak transcription	Lung	lung
5	chr3:88205800-88232400	Weak transcription	Left Ventricle	heart
6	chr3:88206000-88226800	Weak transcription	Ovary	ovary
7	chr3:88206000-88229800	Weak transcription	Thymus	Thymus
8	chr3:88206800-88223400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:88207400-88222200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:88208200-88224600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:88208200-88226600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:88209200-88226400	Weak transcription	Primary B cells from cord blood	blood
13	chr3:88209200-88227800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:88211000-88223800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:88212200-88222800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:88215400-88227000	Weak transcription	HSMM	muscle
17	chr3:88216200-88222000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr3:88220600-88223200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:88220800-88223400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:88220800-88229800	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links