Variant report

Variant	rs4383020
Chromosome Location	chr13:96521060-96521061
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96520254..96522290-chr13:96547977..96549685,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10508027	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11619636	0.81[ASN][1000 genomes]
rs12428062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12430152	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1330556	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1330557	0.95[ASN][1000 genomes]
rs16951334	0.82[CHD][hapmap]
rs16951448	0.81[ASN][1000 genomes]
rs1788062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1854758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3099362	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3099363	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3101570	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs3125431	0.84[EUR][1000 genomes]
rs3886352	0.91[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs4254181	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4347496	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4409947	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4526890	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4773932	0.81[ASN][1000 genomes]
rs531549	0.81[ASN][1000 genomes]
rs537463	0.81[ASN][1000 genomes]
rs56077337	0.81[ASN][1000 genomes]
rs565297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs565898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6492822	0.88[EUR][1000 genomes]
rs661544	0.81[ASN][1000 genomes]
rs662884	0.81[ASN][1000 genomes]
rs72636541	1.00[ASN][1000 genomes]
rs72636556	0.95[ASN][1000 genomes]
rs72636562	0.93[ASN][1000 genomes]
rs72636570	0.95[ASN][1000 genomes]
rs7316996	0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs7318892	0.83[CHD][hapmap];0.87[MEX][hapmap]
rs7323408	1.00[JPT][hapmap]
rs7331211	1.00[JPT][hapmap]
rs7331549	1.00[JPT][hapmap]
rs7332078	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7334320	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7335209	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7339059	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7999737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8000018	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816142	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9516621	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9525077	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9525079	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9584324	1.00[JPT][hapmap]
rs9590328	0.91[EUR][1000 genomes]
rs9590331	0.84[EUR][1000 genomes]
rs9590344	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4383020	GPC5	cis	parietal	SCAN
rs4383020	DZIP1	cis	parietal	SCAN
rs4383020	UGGT2	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
2	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:96498400-96549800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:96502000-96522400	Weak transcription	Colon Smooth Muscle	Colon
5	chr13:96502400-96535400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:96502600-96552600	Weak transcription	Brain Germinal Matrix	brain
7	chr13:96502800-96562600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr13:96503000-96522600	Weak transcription	Aorta	Aorta
9	chr13:96503000-96522600	Weak transcription	Pancreas	Pancrea
10	chr13:96503000-96523600	Weak transcription	Esophagus	oesophagus
11	chr13:96503000-96526800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr13:96503000-96527200	Weak transcription	Fetal Kidney	kidney
13	chr13:96503000-96567400	Weak transcription	NHEK	skin
14	chr13:96503200-96522600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:96503200-96522800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr13:96503200-96527800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:96503200-96535200	Weak transcription	HepG2	liver
18	chr13:96503200-96542000	Weak transcription	Brain Substantia Nigra	brain
19	chr13:96503200-96542000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr13:96503200-96542200	Weak transcription	Brain Hippocampus Middle	brain
21	chr13:96503200-96558000	Weak transcription	NHDF-Ad	bronchial
22	chr13:96503200-96558200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:96503200-96558800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr13:96503400-96521800	Weak transcription	HSMMtube	muscle
25	chr13:96503400-96522600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:96503400-96528600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr13:96503400-96542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:96503400-96555400	Weak transcription	Fetal Heart	heart
29	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:96503600-96528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr13:96503600-96528600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr13:96503600-96559000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:96503600-96562800	Weak transcription	Fetal Brain Female	brain
34	chr13:96503800-96522600	Weak transcription	Left Ventricle	heart
35	chr13:96503800-96522800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr13:96503800-96526800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr13:96503800-96548200	Weak transcription	A549	lung
38	chr13:96504000-96528600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr13:96504000-96534000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr13:96505200-96522400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:96505400-96522400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:96506400-96522600	Weak transcription	Fetal Intestine Large	intestine
43	chr13:96506600-96522600	Weak transcription	Liver	Liver
44	chr13:96506600-96554800	Weak transcription	GM12878-XiMat	blood
45	chr13:96506800-96521600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr13:96506800-96528400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:96506800-96528800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr13:96506800-96536000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr13:96507000-96528600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr13:96510800-96522400	Weak transcription	Ovary	ovary

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