Variant report

Variant	rs4939701
Chromosome Location	chr18:45565774-45565775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45563962..45566776-chr18:45685192..45687168,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12605978	0.92[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs4359513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4468699	0.89[EUR][1000 genomes]
rs4620750	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4940197	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4940202	0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4940217	0.91[EUR][1000 genomes]
rs7226941	0.91[EUR][1000 genomes]
rs8093883	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8099419	0.81[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9945580	0.87[EUR][1000 genomes]
rs9951809	0.89[EUR][1000 genomes]
rs9958955	0.89[EUR][1000 genomes]
rs9960301	0.90[EUR][1000 genomes]
rs9960608	0.80[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	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4939701	SMAD2	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45554200-45567800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr18:45554400-45567600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr18:45557400-45570000	Weak transcription	Fetal Intestine Small	intestine
4	chr18:45558400-45578400	Weak transcription	Ovary	ovary
5	chr18:45560200-45566400	Genic enhancers	Esophagus	oesophagus
6	chr18:45562600-45566800	Weak transcription	Aorta	Aorta
7	chr18:45563800-45565800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr18:45564200-45565800	Weak transcription	Hela-S3	cervix
9	chr18:45564200-45566800	Weak transcription	Dnd41	blood
10	chr18:45564200-45568000	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr18:45564400-45567400	Strong transcription	Gastric	stomach
12	chr18:45564400-45568800	Weak transcription	Right Atrium	heart
13	chr18:45564400-45576000	Weak transcription	Stomach Mucosa	stomach
14	chr18:45564600-45566800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:45564600-45567000	Weak transcription	Pancreas	Pancrea
16	chr18:45564600-45569200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:45564800-45565800	Weak transcription	Fetal Muscle Leg	muscle
18	chr18:45564800-45567200	Strong transcription	Fetal Stomach	stomach
19	chr18:45564800-45572000	Weak transcription	Placenta	Placenta
20	chr18:45565200-45567200	Strong transcription	Colonic Mucosa	Colon
21	chr18:45565200-45567200	Weak transcription	Lung	lung
22	chr18:45565200-45567400	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr18:45565400-45566000	Weak transcription	Spleen	Spleen
24	chr18:45565400-45566800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr18:45565600-45565800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:45565600-45565800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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