Variant report

Variant	rs6676810
Chromosome Location	chr1:169751301-169751302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169453908..169455963-chr1:169751227..169752986,2	K562	blood:
2	chr1:169751112..169752655-chr1:169758575..169760981,2	MCF-7	breast:
3	chr1:169750643..169754945-chr1:169761592..169765030,6	MCF-7	breast:
4	chr1:169749828..169751935-chr1:169761996..169767099,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000460	Chromatin interaction
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10733054	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737549	0.81[EUR][1000 genomes]
rs10753792	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753793	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10800479	0.84[EUR][1000 genomes]
rs10800480	0.84[EUR][1000 genomes]
rs10800481	0.84[EUR][1000 genomes]
rs10800483	0.84[EUR][1000 genomes]
rs10800485	0.81[EUR][1000 genomes]
rs10919230	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919245	0.84[EUR][1000 genomes]
rs10919248	0.84[EUR][1000 genomes]
rs10919251	0.84[EUR][1000 genomes]
rs12133843	0.80[EUR][1000 genomes]
rs1534904	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1883436	0.80[EUR][1000 genomes]
rs2056981	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2179396	0.83[EUR][1000 genomes]
rs2205850	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2205851	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281039	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2294322	0.84[EUR][1000 genomes]
rs2420512	0.84[EUR][1000 genomes]
rs3766132	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3766134	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3766137	0.84[EUR][1000 genomes]
rs3766142	0.81[EUR][1000 genomes]
rs3766148	0.81[EUR][1000 genomes]
rs3917390	0.83[EUR][1000 genomes]
rs3917412	0.82[ASN][1000 genomes]
rs3917434	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4508080	0.81[EUR][1000 genomes]
rs4614317	0.84[EUR][1000 genomes]
rs4656196	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656716	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4656721	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6427217	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427225	0.83[EUR][1000 genomes]
rs6656965	0.83[EUR][1000 genomes]
rs6680508	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680650	0.84[EUR][1000 genomes]
rs6682835	0.82[EUR][1000 genomes]
rs6683056	0.82[EUR][1000 genomes]
rs717481	0.83[EUR][1000 genomes]
rs732185	0.80[EUR][1000 genomes]
rs7515714	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518441	0.83[ASN][1000 genomes]
rs7525259	0.80[EUR][1000 genomes]
rs7526261	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530237	0.81[EUR][1000 genomes]
rs7538317	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7545011	0.84[EUR][1000 genomes]
rs9287097	0.80[EUR][1000 genomes]
rs964827	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6676810	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs6676810	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169748200-169753600	Enhancers	HUVEC	blood vessel
2	chr1:169748400-169751400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:169749000-169751400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr1:169749000-169751600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:169749000-169751600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:169749400-169752000	Enhancers	NHEK	skin
7	chr1:169749400-169761400	Weak transcription	Liver	Liver
8	chr1:169750000-169752400	Enhancers	Placenta	Placenta
9	chr1:169750200-169753000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:169750400-169754400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:169750600-169751400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:169750600-169751600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:169750600-169752000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:169750800-169752000	Enhancers	HMEC	breast
15	chr1:169750800-169762800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:169751000-169751600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:169751000-169752000	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr1:169751200-169751400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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