Variant report

Variant	rs1787180
Chromosome Location	chr18:45351643-45351644
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45349519..45352023-chr18:45354635..45356622,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMAD2-1	chr18:45346666-45352656	XLOC_012839

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10853560	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs11082638	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs11082639	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs12454094	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12455876	0.81[EUR][1000 genomes]
rs12458238	0.88[CEU][hapmap]
rs12956483	0.83[EUR][1000 genomes]
rs12968107	0.92[CEU][hapmap]
rs12968493	0.88[CEU][hapmap]
rs12969725	0.88[CEU][hapmap]
rs13381619	0.91[CHB][hapmap]
rs1502606	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1539872	0.92[CEU][hapmap]
rs1573363	0.92[CEU][hapmap]
rs1613672	0.96[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs1623734	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1625400	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1627974	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.84[YRI][hapmap]
rs17741998	0.92[CEU][hapmap]
rs1787176	0.96[CEU][hapmap];0.92[CHB][hapmap];0.81[EUR][1000 genomes]
rs1787183	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787185	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1787186	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1787189	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1787190	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1787193	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[YRI][hapmap]
rs1792653	0.83[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs1792659	0.87[EUR][1000 genomes]
rs1792665	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792668	0.88[CEU][hapmap]
rs1792669	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs1792670	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs1792671	0.96[CEU][hapmap];0.92[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792674	0.92[CEU][hapmap]
rs1792675	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1792676	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792677	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1792678	0.83[EUR][1000 genomes]
rs1792679	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792680	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792681	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792682	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792683	0.87[CEU][hapmap];0.83[CHB][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs1792686	0.95[CEU][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792687	0.92[CEU][hapmap]
rs1792688	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1847173	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1981	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2012555	0.92[CEU][hapmap]
rs2047778	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2096932	0.84[CHB][hapmap];0.93[YRI][hapmap]
rs2096933	0.93[YRI][hapmap]
rs2852972	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28548478	0.82[EUR][1000 genomes]
rs3813068	0.88[CEU][hapmap];0.96[YRI][hapmap]
rs4940102	0.88[CEU][hapmap]
rs4940109	0.80[CEU][hapmap]
rs62086544	0.83[EUR][1000 genomes]
rs6507790	0.84[CEU][hapmap];0.96[YRI][hapmap]
rs6507791	0.92[CEU][hapmap];0.93[YRI][hapmap]
rs7228393	0.84[CEU][hapmap];0.91[CHB][hapmap]
rs7231538	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs7233129	0.92[CEU][hapmap]
rs7236177	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs729112	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs747952	0.92[CEU][hapmap]
rs747953	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs765213	0.85[CHB][hapmap];0.93[YRI][hapmap]
rs8095519	0.80[CEU][hapmap]
rs8097580	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs8097912	0.92[CEU][hapmap]
rs8099127	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs8099681	0.81[EUR][1000 genomes]
rs948602	0.88[CEU][hapmap]
rs948603	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs948604	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs9946556	0.96[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes]
rs9955626	0.92[CEU][hapmap]
rs9966964	0.87[CEU][hapmap];0.96[YRI][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1787180	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45327400-45358400	Weak transcription	HSMMtube	muscle
2	chr18:45327600-45352600	Weak transcription	Fetal Brain Female	brain
3	chr18:45332200-45352400	Weak transcription	Adipose Nuclei	Adipose
4	chr18:45332600-45351800	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:45333000-45357200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr18:45335400-45365600	Weak transcription	Gastric	stomach
7	chr18:45337600-45357200	Weak transcription	Dnd41	blood
8	chr18:45339600-45359800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr18:45340200-45351800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr18:45340400-45369400	Weak transcription	Fetal Stomach	stomach
11	chr18:45341000-45364200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr18:45341400-45351800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr18:45342200-45384200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr18:45342400-45353800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr18:45342400-45365400	Weak transcription	Psoas Muscle	Psoas
16	chr18:45343400-45351800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr18:45344000-45361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr18:45344000-45373000	Weak transcription	Pancreas	Pancrea
19	chr18:45344200-45364800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr18:45344200-45364800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr18:45344400-45359800	Weak transcription	NHDF-Ad	bronchial
22	chr18:45344400-45365400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr18:45344400-45365600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr18:45344600-45358400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr18:45344600-45365400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr18:45344600-45368000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr18:45344800-45352400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr18:45344800-45362400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr18:45345000-45352600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr18:45345000-45358400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr18:45345000-45368000	Weak transcription	Colon Smooth Muscle	Colon
32	chr18:45345200-45365400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr18:45345400-45351800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr18:45345400-45352200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr18:45345400-45352400	Weak transcription	Fetal Kidney	kidney
36	chr18:45345400-45352600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr18:45345400-45363400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr18:45345600-45352200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr18:45345600-45352800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr18:45346000-45357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr18:45346200-45353800	Weak transcription	Fetal Intestine Large	intestine
43	chr18:45346400-45358400	Weak transcription	HSMM	muscle
44	chr18:45346400-45365600	Weak transcription	Esophagus	oesophagus
45	chr18:45346600-45352400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr18:45346600-45355600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr18:45346600-45361400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr18:45347600-45381800	Weak transcription	Right Ventricle	heart
49	chr18:45348200-45366200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr18:45348400-45359800	Weak transcription	Primary monocytes fromperipheralblood	blood

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