Variant report

Variant	rs1787183
Chromosome Location	chr18:45346932-45346933
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	0.93[CEU][hapmap];0.93[CHB][hapmap]
rs11082638	0.92[CEU][hapmap];0.93[CHB][hapmap]
rs11082639	0.83[CEU][hapmap];0.93[CHB][hapmap]
rs11082641	0.80[CEU][hapmap]
rs12454094	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12458238	0.89[CEU][hapmap]
rs12968107	0.93[CEU][hapmap]
rs12968493	0.89[CEU][hapmap]
rs12969725	0.89[CEU][hapmap]
rs13381619	1.00[CHB][hapmap]
rs1502606	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1539871	0.81[JPT][hapmap]
rs1539872	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs1573363	0.93[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs1613672	0.96[CEU][hapmap];0.93[CHB][hapmap]
rs1623734	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1625400	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1627974	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs17741998	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs1787176	0.96[CEU][hapmap];0.93[CHB][hapmap]
rs1787180	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787185	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787186	0.92[CEU][hapmap]
rs1787189	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1787190	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1787193	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1787194	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1792655	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1792659	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792663	0.82[EUR][1000 genomes]
rs1792664	0.82[EUR][1000 genomes]
rs1792665	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792668	0.89[CEU][hapmap]
rs1792669	0.93[CEU][hapmap];0.93[CHB][hapmap]
rs1792670	0.92[CEU][hapmap];0.93[CHB][hapmap]
rs1792671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792674	0.92[CEU][hapmap]
rs1792675	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs1792676	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792677	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792679	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792680	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792681	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792682	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792683	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs1792686	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792687	0.92[CEU][hapmap]
rs1792688	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1847173	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1981	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2000708	0.80[CEU][hapmap]
rs2000709	0.81[JPT][hapmap]
rs2012555	0.92[CEU][hapmap]
rs2047778	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2096932	0.87[CHB][hapmap]
rs2096933	0.80[CEU][hapmap]
rs2852972	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3813068	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs4940102	0.89[CEU][hapmap]
rs4940109	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs4940110	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs6507790	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs6507791	0.93[CEU][hapmap]
rs7228393	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs7231538	0.93[CEU][hapmap];0.93[CHB][hapmap]
rs7233129	0.93[CEU][hapmap]
rs7236177	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs729112	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs747952	0.93[CEU][hapmap]
rs747953	0.93[CEU][hapmap];0.93[CHB][hapmap]
rs765213	0.94[CHB][hapmap]
rs8095519	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs8097580	0.92[CEU][hapmap];0.84[CHB][hapmap]
rs8097912	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs8099127	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs948602	0.89[CEU][hapmap]
rs948603	0.93[CEU][hapmap]
rs948604	0.82[CEU][hapmap];0.93[CHB][hapmap]
rs9946556	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9955626	0.93[CEU][hapmap]
rs9966964	0.89[CEU][hapmap];0.81[JPT][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
rs1787183	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 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	chr18:45328600-45351600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr18:45332200-45352400	Weak transcription	Adipose Nuclei	Adipose
5	chr18:45332600-45351800	Weak transcription	Fetal Muscle Leg	muscle
6	chr18:45332800-45351600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr18:45333000-45357200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr18:45333800-45351600	Weak transcription	A549	lung
9	chr18:45334600-45349800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr18:45335400-45365600	Weak transcription	Gastric	stomach
11	chr18:45335800-45351600	Weak transcription	Fetal Thymus	thymus
12	chr18:45336400-45351600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:45336600-45351600	Weak transcription	Thymus	Thymus
14	chr18:45337600-45357200	Weak transcription	Dnd41	blood
15	chr18:45339600-45359800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr18:45340200-45351800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:45340400-45369400	Weak transcription	Fetal Stomach	stomach
18	chr18:45340800-45347800	Weak transcription	Hela-S3	cervix
19	chr18:45341000-45364200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr18:45341400-45351800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr18:45342200-45384200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr18:45342400-45353800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr18:45342400-45365400	Weak transcription	Psoas Muscle	Psoas
24	chr18:45342600-45349200	Weak transcription	Primary T cells from cord blood	blood
25	chr18:45342600-45351600	Weak transcription	Left Ventricle	heart
26	chr18:45343200-45351600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr18:45343400-45351800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr18:45343800-45351600	Weak transcription	Lung	lung
29	chr18:45344000-45361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:45344000-45373000	Weak transcription	Pancreas	Pancrea
31	chr18:45344200-45364800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:45344200-45364800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr18:45344400-45359800	Weak transcription	NHDF-Ad	bronchial
34	chr18:45344400-45365400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr18:45344400-45365600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:45344600-45351600	Weak transcription	Fetal Lung	lung
37	chr18:45344600-45358400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr18:45344600-45365400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr18:45344600-45368000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr18:45344800-45352400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr18:45344800-45362400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr18:45345000-45351600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr18:45345000-45351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr18:45345000-45352600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr18:45345000-45358400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr18:45345000-45368000	Weak transcription	Colon Smooth Muscle	Colon
47	chr18:45345200-45365400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:45345400-45351800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr18:45345400-45352200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr18:45345400-45352400	Weak transcription	Fetal Kidney	kidney

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