Variant report

Variant	rs1787186
Chromosome Location	chr18:45371509-45371510
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	chr18:45370062..45371817-chr18:45453252..45455227,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10502890	0.93[ASW][hapmap];0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs10853560	0.92[CEU][hapmap]
rs11082638	0.92[CEU][hapmap]
rs11082639	0.84[CEU][hapmap]
rs11082641	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs12455876	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12457664	0.93[ASW][hapmap];0.85[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs12458238	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs12955534	0.93[EUR][1000 genomes]
rs12968107	0.91[CEU][hapmap]
rs12968493	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs12969725	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs1502606	0.82[EUR][1000 genomes]
rs1539871	0.86[LWK][hapmap]
rs1539872	0.92[CEU][hapmap]
rs1573362	0.85[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs1573363	0.92[CEU][hapmap]
rs1613672	0.96[CEU][hapmap]
rs1623734	0.81[EUR][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs17741998	0.92[CEU][hapmap]
rs1787176	0.96[CEU][hapmap]
rs1787180	0.82[EUR][1000 genomes]
rs1787185	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1787190	0.83[EUR][1000 genomes]
rs1787193	0.96[CEU][hapmap]
rs1787194	0.96[CEU][hapmap]
rs1787198	0.81[AMR][1000 genomes]
rs1787199	0.86[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap]
rs1792655	0.96[CEU][hapmap]
rs1792658	0.81[LWK][hapmap]
rs1792659	0.81[EUR][1000 genomes]
rs1792663	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792664	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792666	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792667	0.81[AMR][1000 genomes]
rs1792668	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes]
rs1792669	0.92[CEU][hapmap]
rs1792670	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs1792671	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1792674	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs1792675	0.96[CEU][hapmap]
rs1792678	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792679	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1792680	0.83[EUR][1000 genomes]
rs1792681	0.92[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs1792682	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1792683	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs1792684	0.87[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792686	0.87[ASW][hapmap];0.96[CEU][hapmap];0.92[LWK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1792687	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes]
rs1792688	0.84[EUR][1000 genomes]
rs1792689	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs1847173	0.81[EUR][1000 genomes]
rs1942158	0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs1981	0.92[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2000708	0.80[CEU][hapmap]
rs2012555	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap]
rs2096933	0.80[CEU][hapmap]
rs2653659	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2852972	0.81[EUR][1000 genomes]
rs3813068	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs4940102	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs4940109	0.80[CEU][hapmap]
rs4940110	0.80[CEU][hapmap]
rs6507790	0.84[CEU][hapmap]
rs6507791	0.92[CEU][hapmap]
rs7228393	0.84[CEU][hapmap]
rs7231538	0.92[CEU][hapmap]
rs7233129	0.92[CEU][hapmap]
rs7236177	0.92[CEU][hapmap]
rs729112	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs747952	0.92[CEU][hapmap]
rs747953	0.92[CEU][hapmap]
rs8095519	0.80[CEU][hapmap]
rs8097580	0.91[CEU][hapmap]
rs8097912	0.92[CEU][hapmap]
rs8099127	0.92[CEU][hapmap]
rs8671	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs948602	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap]
rs948603	0.91[CEU][hapmap]
rs948604	0.80[CEU][hapmap]
rs9946556	0.96[CEU][hapmap]
rs9955626	0.92[CEU][hapmap]
rs9966964	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057722	chr18:45343965-45401360	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1058673	chr18:45360012-45404492	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1059186	chr18:45360012-45407405	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1062894	chr18:45368587-45387738	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1066394	chr18:45368587-45394386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1060581	chr18:45368587-45397623	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv1057525	chr18:45368587-45407405	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
8	nsv1064282	chr18:45369857-45404768	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1787186	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45342200-45384200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:45344000-45373000	Weak transcription	Pancreas	Pancrea
3	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:45347600-45381800	Weak transcription	Right Ventricle	heart
5	chr18:45351000-45374600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr18:45353000-45381200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr18:45354600-45381800	Weak transcription	Fetal Intestine Small	intestine
8	chr18:45355600-45375600	Strong transcription	Hela-S3	cervix
9	chr18:45355600-45375800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr18:45355600-45376200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:45356000-45378000	Weak transcription	Small Intestine	intestine
12	chr18:45356200-45377800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:45356200-45384000	Weak transcription	Spleen	Spleen
14	chr18:45356600-45376200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr18:45357200-45373200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr18:45358600-45376400	Strong transcription	Dnd41	blood
17	chr18:45358800-45382400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr18:45359000-45374400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr18:45359800-45375600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr18:45359800-45375600	Strong transcription	Fetal Thymus	thymus
21	chr18:45360000-45373200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr18:45360000-45375400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr18:45360000-45375600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr18:45361400-45375600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr18:45361400-45375600	Strong transcription	A549	lung
26	chr18:45361400-45376000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr18:45362400-45373000	Strong transcription	Placenta	Placenta
28	chr18:45362400-45375200	Strong transcription	Primary B cells from cord blood	blood
29	chr18:45362400-45375600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr18:45362600-45371800	Strong transcription	Liver	Liver
31	chr18:45362600-45372400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr18:45362600-45375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr18:45363000-45375800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr18:45363400-45373600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr18:45363800-45375600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr18:45363800-45375600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr18:45363800-45376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr18:45364000-45372200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:45364000-45375400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr18:45364400-45375600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr18:45364600-45375600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr18:45364600-45376200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr18:45364800-45372400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:45364800-45372600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr18:45365000-45373200	Strong transcription	Fetal Lung	lung
46	chr18:45365000-45373400	Strong transcription	Adipose Nuclei	Adipose
47	chr18:45365200-45373600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr18:45365200-45375800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr18:45365400-45372400	Strong transcription	HepG2	liver
50	chr18:45365400-45375000	Strong transcription	GM12878-XiMat	blood

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