Variant report

Variant	rs6468801
Chromosome Location	chr8:102840673-102840674
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:97272466..97274308-chr8:102840170..102842402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156469	Chromatin interaction
ENSG00000156471	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1074703	0.87[ASN][1000 genomes]
rs10808379	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1111886	0.80[TSI][hapmap]
rs12334693	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs12544026	0.80[EUR][1000 genomes]
rs1264933	0.92[CEU][hapmap]
rs12677525	0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs13251735	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13255004	0.96[EUR][1000 genomes]
rs1465167	0.87[CHD][hapmap]
rs17406994	0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1893366	0.92[CEU][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs2155942	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2155943	0.91[EUR][1000 genomes]
rs2226724	0.92[EUR][1000 genomes]
rs2226725	0.95[EUR][1000 genomes]
rs28837777	0.85[EUR][1000 genomes]
rs4576401	0.85[EUR][1000 genomes]
rs4734595	0.90[TSI][hapmap]
rs4734596	0.86[EUR][1000 genomes]
rs4734597	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6468793	0.84[EUR][1000 genomes]
rs6468794	0.85[EUR][1000 genomes]
rs6468795	0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs6468796	0.85[EUR][1000 genomes]
rs6468798	0.84[EUR][1000 genomes]
rs6468799	0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6984260	0.82[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6988793	0.84[CHD][hapmap]
rs6993577	0.96[EUR][1000 genomes]
rs7000357	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7008826	0.80[TSI][hapmap]
rs7009385	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs7011941	0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7012512	0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs7015311	0.85[EUR][1000 genomes]
rs7813132	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7827304	0.87[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7827691	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7827941	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7828175	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs7830291	0.87[CHD][hapmap]
rs7835223	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7838696	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8181022	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs8181025	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9297313	0.92[CEU][hapmap]

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	nsv1018653	chr8:102818271-103009082	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539700	chr8:102818271-103009082	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6468801	NCALD	cis	parietal	SCAN
rs6468801	C8orf56	cis	parietal	SCAN
rs6468801	FOXL1	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102803600-102870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:102832200-102843800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:102834800-102843800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:102835000-102844400	Weak transcription	Psoas Muscle	Psoas
5	chr8:102835000-102852000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:102836200-102844400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:102836600-102844000	Weak transcription	Fetal Heart	heart
8	chr8:102836600-102844200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr8:102836800-102843800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:102837200-102844000	Weak transcription	Brain Angular Gyrus	brain
11	chr8:102837800-102843800	Weak transcription	Aorta	Aorta
12	chr8:102838600-102848400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr8:102839400-102840800	Enhancers	Adipose Nuclei	Adipose
14	chr8:102839600-102843800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr8:102840400-102843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:102840400-102843800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr8:102840400-102843800	Weak transcription	Left Ventricle	heart
18	chr8:102840400-102843800	Weak transcription	NHDF-Ad	bronchial
19	chr8:102840400-102844000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr8:102840400-102844200	Weak transcription	HSMMtube	muscle
21	chr8:102840400-102844400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:102840600-102843800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr8:102840600-102844000	Weak transcription	Fetal Muscle Leg	muscle
24	chr8:102840600-102844200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links