Variant report

Variant	rs7333
Chromosome Location	chr1:59041220-59041221
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
ENSG00000173406	Chromatin interaction
ENSG00000162600	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
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[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];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[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2271005	0.86[ASN][1000 genomes]
rs232835	0.97[ASN][1000 genomes]
rs232840	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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]
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];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs6683669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6686976	0.86[ASN][1000 genomes]
rs725907	0.86[ASN][1000 genomes]
rs72672292	1.00[ASN][1000 genomes]
rs729084	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7535313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs7537470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7333	C1orf175	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59038400-59043600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr1:59040000-59041800	Active TSS	Pancreas	Pancrea
3	chr1:59040000-59042000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:59040000-59042000	Active TSS	Stomach Mucosa	stomach
5	chr1:59040200-59043400	Active TSS	NHEK	skin
6	chr1:59040200-59043600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:59040600-59041600	Flanking Active TSS	HUVEC	blood vessel
8	chr1:59040600-59042000	Bivalent/Poised TSS	Fetal Stomach	stomach
9	chr1:59040800-59043400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:59040800-59043400	Active TSS	Placenta Amnion	Placenta Amnion
11	chr1:59041000-59041800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr1:59041000-59043200	Active TSS	HMEC	breast
13	chr1:59041200-59041400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
14	chr1:59041200-59041400	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
15	chr1:59041200-59041400	Flanking Active TSS	Hela-S3	cervix
16	chr1:59041200-59041600	Enhancers	Brain Substantia Nigra	brain
17	chr1:59041200-59041600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:59041200-59041800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
19	chr1:59041200-59042000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:59041200-59042200	Transcr. at gene 5' and 3'	Esophagus	oesophagus
21	chr1:59041200-59042200	Active TSS	Lung	lung
22	chr1:59041200-59042800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:59041200-59043200	ZNF genes & repeats	GM12878-XiMat	blood
24	chr1:59041200-59044200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links