Variant report

Variant	rs7776980
Chromosome Location	chr7:117496319-117496320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117488313..117490003-chr7:117495202..117498035,2	MCF-7	breast:
2	chr7:117488843..117491643-chr7:117493706..117497041,3	K562	blood:
3	7:115847372-115857098..7:117493134-117497089	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10244364	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10252771	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10259910	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10263711	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10267771	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10272923	0.83[GIH][hapmap]
rs10276758	0.81[EUR][1000 genomes]
rs10487380	0.81[EUR][1000 genomes]
rs13239186	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1548460	0.86[GIH][hapmap]
rs34031516	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34212554	0.91[ASN][1000 genomes]
rs34298216	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34564710	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34729439	0.80[EUR][1000 genomes]
rs6943120	0.86[GIH][hapmap]
rs6952555	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6961907	0.82[EUR][1000 genomes]
rs6966339	0.86[GIH][hapmap]
rs6976111	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs727164	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7782815	0.81[EUR][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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7776980	ING3	cis	parietal	SCAN
rs7776980	CTTNBP2	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117469000-117503600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:117469400-117503800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:117469600-117511800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:117475600-117496600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:117475600-117506600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:117476000-117501000	Weak transcription	Fetal Stomach	stomach
7	chr7:117476200-117497200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:117478400-117502600	Weak transcription	Pancreas	Pancrea
9	chr7:117481600-117502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:117483800-117501000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:117484200-117503800	Weak transcription	Fetal Kidney	kidney
12	chr7:117484400-117501000	Weak transcription	Adipose Nuclei	Adipose
13	chr7:117484400-117510800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr7:117484800-117503600	Weak transcription	Aorta	Aorta
15	chr7:117485000-117501000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:117485200-117499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:117489400-117503800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr7:117489400-117511800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:117489800-117498600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr7:117489800-117499600	Weak transcription	NHLF	lung
21	chr7:117490400-117498600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:117490400-117508000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:117490400-117508000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:117491200-117502000	Weak transcription	Fetal Heart	heart
25	chr7:117491800-117496800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr7:117493200-117502000	Weak transcription	Brain Anterior Caudate	brain
27	chr7:117493400-117499600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:117494200-117501800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:117494200-117502000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:117494600-117501400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:117494600-117501400	Weak transcription	Fetal Brain Male	brain
32	chr7:117495000-117502000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr7:117495200-117496400	Strong transcription	Brain Germinal Matrix	brain
34	chr7:117495200-117496400	Strong transcription	Fetal Brain Female	brain
35	chr7:117495200-117496400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr7:117495200-117501000	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:117495800-117503600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr7:117496000-117496600	Strong transcription	Brain Angular Gyrus	brain
39	chr7:117496000-117497200	Enhancers	Fetal Lung	lung
40	chr7:117496200-117496400	Genic enhancers	Brain Substantia Nigra	brain
41	chr7:117496200-117496600	Enhancers	Fetal Intestine Small	intestine

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