Variant report

Variant	rs6706297
Chromosome Location	chr2:173038675-173038676
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173037340..173040256-chr2:173329062..173331322,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232788	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10183800	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10186626	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389254	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13400011	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432384	1.00[ASN][1000 genomes]
rs62182093	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6433333	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6718762	0.95[ASN][1000 genomes]
rs6738987	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751639	1.00[ASN][1000 genomes]
rs6751644	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607929	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875413	chr2:173009413-173097343	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv2762294	chr2:173028656-173071270	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6706297	BBS5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173037800-173043000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:173038000-173038800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
3	chr2:173038000-173042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:173038000-173043000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:173038200-173042400	Weak transcription	NH-A	brain
6	chr2:173038200-173042600	Weak transcription	HMEC	breast
7	chr2:173038200-173043400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr2:173038200-173045200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:173038400-173038800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:173038400-173042200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:173038400-173042400	Weak transcription	NHEK	skin
12	chr2:173038400-173042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:173038400-173043600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:173038400-173043800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:173038400-173044000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:173038400-173044000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:173038600-173038800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
18	chr2:173038600-173039000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:173038600-173043600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:173038600-173044000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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