Variant report

Variant	rs12769135
Chromosome Location	chr10:95971466-95971467
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10509669	0.82[MEX][hapmap]
rs35632833	0.86[ASN][1000 genomes]
rs4918159	0.85[ASN][1000 genomes]
rs71480896	0.87[ASN][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	nsv1036676	chr10:95851376-96103876	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12769135	TMEM20	cis	parietal	SCAN
rs12769135	NOC3L	cis	parietal	SCAN
rs12769135	RPP30	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95933000-95972600	Weak transcription	Fetal Intestine Large	intestine
2	chr10:95941200-95979800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr10:95943400-95973800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:95959600-95972400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr10:95959800-95972800	Weak transcription	A549	lung
6	chr10:95960000-95991800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:95962600-95973600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr10:95965200-95972600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:95965800-95972800	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:95966600-95987000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr10:95967000-95972400	Weak transcription	Liver	Liver
12	chr10:95967400-95988000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:95968000-95971800	Enhancers	Fetal Lung	lung
14	chr10:95968800-95972600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:95968800-95972800	Weak transcription	NHLF	lung
16	chr10:95969400-95971800	Enhancers	Fetal Stomach	stomach
17	chr10:95969600-95974200	Enhancers	HSMMtube	muscle
18	chr10:95969600-95974400	Enhancers	Fetal Muscle Leg	muscle
19	chr10:95970200-95971600	Enhancers	Psoas Muscle	Psoas
20	chr10:95970200-95973200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr10:95970400-95971600	Enhancers	Aorta	Aorta
22	chr10:95970800-96005800	Weak transcription	Colonic Mucosa	Colon
23	chr10:95971000-95994000	Weak transcription	Gastric	stomach
24	chr10:95971200-95972400	Weak transcription	Small Intestine	intestine
25	chr10:95971200-95972600	Weak transcription	HepG2	liver
26	chr10:95971200-95972800	Weak transcription	Adipose Nuclei	Adipose
27	chr10:95971200-95972800	Weak transcription	Spleen	Spleen
28	chr10:95971200-95973000	Weak transcription	Ovary	ovary
29	chr10:95971200-95973200	Weak transcription	Lung	lung
30	chr10:95971200-95974000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr10:95971200-95974200	Weak transcription	Left Ventricle	heart
32	chr10:95971200-95974400	Weak transcription	Right Atrium	heart
33	chr10:95971200-95974600	Weak transcription	Fetal Intestine Small	intestine
34	chr10:95971200-95974800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr10:95971200-95977400	Weak transcription	HSMM	muscle
36	chr10:95971200-95979200	Weak transcription	Fetal Heart	heart
37	chr10:95971200-95979600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr10:95971200-95983800	Weak transcription	Pancreas	Pancrea
39	chr10:95971200-95987200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr10:95971400-95972600	Weak transcription	Stomach Smooth Muscle	stomach

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