Variant report

Variant	rs4078254
Chromosome Location	chr5:112456067-112456068
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	chr5:112455253..112458185-chr5:112461323..112464102,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10040400	0.81[ASN][1000 genomes]
rs10067901	0.86[ASN][1000 genomes]
rs10074318	0.80[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs10478110	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11241191	0.91[ASN][1000 genomes]
rs11241192	0.91[ASN][1000 genomes]
rs11241193	0.80[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11743369	0.87[ASN][1000 genomes]
rs11953203	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12188482	0.94[ASN][1000 genomes]
rs12517185	0.80[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12517187	0.91[ASN][1000 genomes]
rs13156718	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13170088	0.83[EUR][1000 genomes]
rs13174483	0.80[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs13179421	0.91[ASN][1000 genomes]
rs13183638	0.85[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs13184187	0.94[ASN][1000 genomes]
rs13190424	0.84[EUR][1000 genomes]
rs1443693	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs36041392	0.94[ASN][1000 genomes]
rs3884576	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3922563	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3922583	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922584	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs3922585	0.84[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs4078252	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs4078253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235793	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4262097	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705542	0.82[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705543	0.82[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4705544	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705545	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705546	0.85[EUR][1000 genomes]
rs4705780	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4705782	0.81[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4705783	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4705786	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4705787	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4705788	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62374710	0.91[ASN][1000 genomes]
rs6594683	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6594687	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs6859963	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6869399	0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6883605	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7700271	0.91[ASN][1000 genomes]
rs7702177	1.00[CEU][hapmap]
rs7704382	0.91[ASN][1000 genomes]
rs7707142	0.86[ASN][1000 genomes]
rs7731180	0.90[ASN][1000 genomes]
rs9326877	0.91[ASN][1000 genomes]
rs9326878	0.80[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9326879	0.80[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs9885385	0.91[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	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4078254	SRP19	cis	parietal	SCAN
rs4078254	AQPEP	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:112450000-112459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:112451000-112460600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:112451000-112478800	Weak transcription	Aorta	Aorta
6	chr5:112451800-112456200	Enhancers	Ovary	ovary
7	chr5:112452600-112456800	Enhancers	Fetal Stomach	stomach
8	chr5:112452800-112456200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:112452800-112456200	Enhancers	Right Ventricle	heart
10	chr5:112452800-112457200	Enhancers	Left Ventricle	heart
11	chr5:112453000-112456200	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr5:112453400-112456200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr5:112453600-112457200	Enhancers	Right Atrium	heart
14	chr5:112453800-112461800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:112454200-112456200	Enhancers	Placenta	Placenta
16	chr5:112454200-112457600	Enhancers	Liver	Liver
17	chr5:112454400-112456200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:112454400-112456200	Enhancers	Fetal Kidney	kidney
19	chr5:112454400-112456200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr5:112454600-112457200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:112454600-112459000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:112454600-112459400	Enhancers	NHDF-Ad	bronchial
23	chr5:112454600-112460600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:112454800-112460400	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:112454800-112460600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:112455000-112456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:112455000-112460000	Weak transcription	Fetal Brain Male	brain
28	chr5:112455000-112462200	Enhancers	Fetal Heart	heart
29	chr5:112455200-112459200	Weak transcription	Pancreas	Pancrea
30	chr5:112455200-112459400	Weak transcription	Brain Germinal Matrix	brain
31	chr5:112455200-112459400	Weak transcription	Fetal Brain Female	brain
32	chr5:112455400-112456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:112455400-112458000	Weak transcription	NHLF	lung
34	chr5:112455400-112458400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:112455400-112459200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:112455400-112459200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:112455400-112459600	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:112455400-112460200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr5:112455400-112461400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:112455400-112461400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:112455600-112456600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:112455600-112456800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:112455600-112456800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:112455600-112457400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:112455600-112457400	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr5:112455600-112457400	Weak transcription	Adipose Nuclei	Adipose
47	chr5:112455600-112458200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:112455600-112460000	Weak transcription	Fetal Lung	lung
49	chr5:112455800-112456200	Weak transcription	HMEC	breast
50	chr5:112455800-112456600	Enhancers	Pancreatic Islets	Pancreatic Islet

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