Variant report

Variant	rs10518378
Chromosome Location	chr4:121661208-121661209
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	chr4:121651698..121654667-chr4:121660319..121662690,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10518376	0.81[YRI][hapmap]
rs17051235	0.86[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17051239	0.85[CHB][hapmap]
rs17346897	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17412142	0.81[YRI][hapmap]
rs6838858	0.81[YRI][hapmap]
rs843573	0.91[EUR][1000 genomes]
rs843575	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879852	chr4:121108734-121768496	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv998094	chr4:121504565-122374203	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1004485	chr4:121542992-121716769	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv916737	chr4:121589793-121748847	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv461634	chr4:121623057-121765527	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv595334	chr4:121623057-121765527	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013704	chr4:121657648-121791601	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10518378	SYNPO2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:121620800-121671400	Weak transcription	Pancreas	Pancrea
2	chr4:121630000-121671400	Weak transcription	Ovary	ovary
3	chr4:121641200-121670400	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:121641400-121669600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:121642800-121670600	Weak transcription	Fetal Stomach	stomach
6	chr4:121645800-121662000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:121647200-121671400	Weak transcription	Fetal Lung	lung
8	chr4:121647400-121670600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:121648200-121671600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:121648200-121671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:121648400-121670600	Weak transcription	Adipose Nuclei	Adipose
12	chr4:121649600-121670800	Weak transcription	Fetal Intestine Large	intestine
13	chr4:121651200-121669200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:121652000-121673600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:121652400-121670800	Weak transcription	Right Ventricle	heart
16	chr4:121652600-121687000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:121653000-121662000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:121653000-121662600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:121653000-121662800	Weak transcription	Lung	lung
20	chr4:121653200-121671600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:121653200-121672200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:121656000-121670600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:121656200-121661600	Weak transcription	Fetal Thymus	thymus
24	chr4:121658800-121668600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr4:121658800-121670600	Weak transcription	Aorta	Aorta
26	chr4:121658800-121671400	Weak transcription	Left Ventricle	heart
27	chr4:121659000-121669600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr4:121660400-121668800	Weak transcription	Muscle Satellite Cultured Cells	--

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