Variant report

Variant	rs7608117
Chromosome Location	chr2:11265972-11265973
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10951206..10953144-chr2:11264871..11266942,2	MCF-7	breast:
2	chr2:11054478..11056999-chr2:11265255..11267127,2	MCF-7	breast:
3	chr2:11237821..11239855-chr2:11264703..11266407,3	MCF-7	breast:
4	chr2:10980632..10983629-chr2:11264384..11266623,2	MCF-7	breast:
5	chr2:11048727..11055858-chr2:11258107..11267123,21	MCF-7	breast:
6	chr2:11263766..11266286-chr2:11293280..11295387,2	K562	blood:
7	chr2:11074952..11076639-chr2:11264485..11265994,2	MCF-7	breast:
8	chr2:11259220..11266280-chr2:11670518..11676450,12	MCF-7	breast:
9	chr2:10971067..10979892-chr2:11260331..11267146,21	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143870	Chromatin interaction
ENSG00000162976	Chromatin interaction
ENSG00000162975	Chromatin interaction
ENSG00000196208	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13002429	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021587	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17366322	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2357993	1.00[ASN][1000 genomes]
rs2357994	1.00[ASN][1000 genomes]
rs7591945	0.91[YRI][hapmap]

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	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	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
rs7608117	C2orf50	cis	parietal	SCAN
rs7608117	IAH1	cis	cerebellum	SCAN
rs7608117	PQLC3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11262200-11269800	Weak transcription	Ovary	ovary
2	chr2:11262800-11268600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:11262800-11269600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:11263000-11268400	Weak transcription	HMEC	breast
5	chr2:11263400-11268000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:11263400-11269800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:11263600-11269800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:11263800-11268000	Weak transcription	Spleen	Spleen
9	chr2:11264600-11268600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:11264600-11269600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:11264800-11269800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:11265000-11268400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:11265000-11268400	Weak transcription	Stomach Mucosa	stomach
14	chr2:11265000-11268600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:11265000-11269400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:11265000-11269800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:11265200-11269600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:11265200-11269800	Weak transcription	Liver	Liver
19	chr2:11265400-11268400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:11265400-11269600	Weak transcription	A549	lung

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