Variant report

Variant	rs2189452
Chromosome Location	chr7:120462955-120462956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:120458622..120460616-chr7:120461070..120463275,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10252911	0.80[CHB][hapmap]
rs10261886	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs17132716	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17143001	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs17143009	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs17143055	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs1859316	0.80[CHB][hapmap]
rs2107276	0.80[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2158323	0.80[ASN][1000 genomes]
rs2158324	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2402551	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3757557	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3779386	0.80[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs3779387	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3779388	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779389	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4141301	1.00[YRI][hapmap]
rs4141309	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4461820	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs56922360	0.82[AFR][1000 genomes]
rs57457261	0.82[AFR][1000 genomes]
rs58686737	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59169713	0.82[AFR][1000 genomes]
rs59567952	0.82[AFR][1000 genomes]
rs60837162	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466761	0.81[CHD][hapmap]
rs6971854	0.80[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs6975372	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs6979247	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs73427805	0.85[ASN][1000 genomes]
rs73427831	0.89[ASN][1000 genomes]
rs73427834	0.87[ASN][1000 genomes]
rs7776721	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs7779136	0.82[AFR][1000 genomes]
rs7779941	0.82[AFR][1000 genomes]
rs7780247	0.82[AFR][1000 genomes]
rs7789807	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7800318	0.83[ASN][1000 genomes]
rs7806629	0.82[AFR][1000 genomes]
rs9648991	0.82[AFR][1000 genomes]
rs9648992	0.82[AFR][1000 genomes]
rs9648993	0.82[AFR][1000 genomes]
rs9649427	0.82[AFR][1000 genomes]
rs9649428	0.82[AFR][1000 genomes]
rs996903	0.81[CHD][hapmap]

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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2189452	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120425600-120470400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:120427400-120466000	Weak transcription	Fetal Stomach	stomach
3	chr7:120430400-120468200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:120432600-120468400	Weak transcription	Lung	lung
5	chr7:120439400-120469200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr7:120446000-120476200	Weak transcription	Left Ventricle	heart
9	chr7:120447400-120471400	Weak transcription	Fetal Kidney	kidney
10	chr7:120447800-120465600	Weak transcription	Liver	Liver
11	chr7:120449800-120476000	Weak transcription	HUVEC	blood vessel
12	chr7:120450600-120470400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:120452800-120476000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:120455000-120465800	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:120455000-120467800	Weak transcription	Fetal Heart	heart
16	chr7:120455600-120468400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:120455600-120472200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:120455800-120465800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:120455800-120474400	Weak transcription	Fetal Intestine Large	intestine
20	chr7:120455800-120476000	Weak transcription	Fetal Muscle Leg	muscle
21	chr7:120458200-120468400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr7:120458400-120475800	Weak transcription	Fetal Intestine Small	intestine
23	chr7:120460200-120465000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:120460400-120469400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr7:120462600-120464000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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