Variant report

Variant	rs10259910
Chromosome Location	chr7:117503982-117503983
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10244364	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10252771	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10263711	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10267771	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10272923	0.83[GIH][hapmap]
rs10276758	0.82[EUR][1000 genomes]
rs10487380	0.82[EUR][1000 genomes]
rs1156954	0.83[CEU][hapmap]
rs13239186	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1548460	0.86[GIH][hapmap]
rs34031516	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34212554	0.88[ASN][1000 genomes]
rs34298216	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34564710	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34729439	0.81[EUR][1000 genomes]
rs6943120	0.86[GIH][hapmap]
rs6952555	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6961907	0.83[EUR][1000 genomes]
rs6966339	0.86[GIH][hapmap]
rs6976111	0.83[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs727164	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7776980	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]
rs7782815	0.81[EUR][1000 genomes]

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	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
2	esv3407409	chr7:117503766-117506314	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10259910	CTTNBP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117469600-117511800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:117475600-117506600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:117484400-117510800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:117489400-117511800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:117490400-117508000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:117490400-117508000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr7:117501400-117504000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:117501400-117504400	Enhancers	Fetal Brain Male	brain
9	chr7:117501400-117507400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:117501400-117507600	Weak transcription	Brain Germinal Matrix	brain
11	chr7:117501600-117506400	Weak transcription	Adipose Nuclei	Adipose
12	chr7:117501600-117507400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr7:117501800-117504400	Enhancers	Brain Substantia Nigra	brain
14	chr7:117501800-117504600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr7:117502000-117504400	Enhancers	Brain Angular Gyrus	brain
16	chr7:117502000-117505400	Enhancers	Brain Anterior Caudate	brain
17	chr7:117502400-117510000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:117502400-117511400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:117502400-117511800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:117502600-117504000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr7:117502600-117504000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr7:117502600-117504400	Enhancers	Brain Cingulate Gyrus	brain
23	chr7:117502800-117508800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:117502800-117511800	Weak transcription	Pancreas	Pancrea
25	chr7:117503000-117504600	Enhancers	Brain Hippocampus Middle	brain
26	chr7:117503400-117504000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr7:117503400-117504000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr7:117503400-117504400	Enhancers	Fetal Brain Female	brain
29	chr7:117503600-117504000	Enhancers	Aorta	Aorta
30	chr7:117503600-117504000	Enhancers	Colon Smooth Muscle	Colon
31	chr7:117503600-117504200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr7:117503600-117504200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:117503600-117504400	Enhancers	NHLF	lung
34	chr7:117503600-117504600	Enhancers	Fetal Lung	lung
35	chr7:117503800-117504000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:117503800-117504000	Enhancers	Fetal Heart	heart
37	chr7:117503800-117504200	Enhancers	Stomach Smooth Muscle	stomach
38	chr7:117503800-117504400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:117503800-117504400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr7:117503800-117504600	Enhancers	Fetal Stomach	stomach
41	chr7:117503800-117510600	Weak transcription	Rectal Smooth Muscle	rectum

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