Variant report

Variant	rs6683669
Chromosome Location	chr1:59041092-59041093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59039544..59041412-chr1:59138456..59140004,2	MCF-7	breast:
2	chr1:59009849..59013755-chr1:59040870..59045611,9	MCF-7	breast:
3	chr1:59039914..59042841-chr1:59125894..59128684,2	MCF-7	breast:
4	chr1:59039784..59042509-chr1:59074910..59077228,3	MCF-7	breast:
5	chr1:59007888..59009563-chr1:59039964..59042756,2	K562	blood:
6	chr1:59003237..59005403-chr1:59039825..59042747,2	MCF-7	breast:
7	chr1:59039584..59041517-chr1:60271631..60274064,2	MCF-7	breast:
8	chr1:58980540..58982714-chr1:59039568..59041235,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162600	Chromatin interaction
ENSG00000173406	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1062964	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs11801938	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11805701	0.86[ASN][1000 genomes]
rs11805835	0.86[ASN][1000 genomes]
rs11807197	0.86[ASN][1000 genomes]
rs11808438	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11809508	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs14008	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096876	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117643	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117650	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117654	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117666	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117681	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117688	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117699	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117714	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117717	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117720	0.88[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117732	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs17117747	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs17117850	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs179798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2268943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271005	0.86[ASN][1000 genomes]
rs232835	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs232840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs338241	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs4912340	0.86[ASN][1000 genomes]
rs4912345	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs4912346	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs58370530	0.83[EUR][1000 genomes]
rs58370911	0.86[ASN][1000 genomes]
rs59493428	0.88[ASN][1000 genomes]
rs60008712	0.88[ASN][1000 genomes]
rs60179866	0.89[ASN][1000 genomes]
rs60614132	0.86[ASN][1000 genomes]
rs61629658	0.86[ASN][1000 genomes]
rs61781815	0.86[ASN][1000 genomes]
rs61781821	0.86[ASN][1000 genomes]
rs61781822	0.86[ASN][1000 genomes]
rs61781823	0.86[ASN][1000 genomes]
rs61781824	0.86[ASN][1000 genomes]
rs6587829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs6674248	0.82[CEU][hapmap]
rs6686976	0.86[ASN][1000 genomes]
rs725907	0.86[ASN][1000 genomes]
rs72672271	0.83[EUR][1000 genomes]
rs72672286	0.83[EUR][1000 genomes]
rs72672292	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72674118	0.83[EUR][1000 genomes]
rs72674121	0.83[EUR][1000 genomes]
rs72674127	0.83[EUR][1000 genomes]
rs729084	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7333	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7535313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7537470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.86[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	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59038000-59041200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:59038400-59043600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:59038600-59041200	Enhancers	Hela-S3	cervix
4	chr1:59039600-59041200	Active TSS	Esophagus	oesophagus
5	chr1:59040000-59041200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
6	chr1:59040000-59041800	Active TSS	Pancreas	Pancrea
7	chr1:59040000-59042000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:59040000-59042000	Active TSS	Stomach Mucosa	stomach
9	chr1:59040200-59043400	Active TSS	NHEK	skin
10	chr1:59040200-59043600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:59040400-59041200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:59040600-59041600	Flanking Active TSS	HUVEC	blood vessel
13	chr1:59040600-59042000	Bivalent/Poised TSS	Fetal Stomach	stomach
14	chr1:59040800-59041200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:59040800-59041200	Weak transcription	GM12878-XiMat	blood
16	chr1:59040800-59043400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:59040800-59043400	Active TSS	Placenta Amnion	Placenta Amnion
18	chr1:59041000-59041800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr1:59041000-59043200	Active TSS	HMEC	breast

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