Variant report

Variant	rs12454094
Chromosome Location	chr18:45336485-45336486
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	chr18:45332755..45334879-chr18:45335286..45338211,2	K562	blood:

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];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11082638	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11082639	0.83[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11082641	0.80[CEU][hapmap]
rs12458238	0.89[CEU][hapmap]
rs12968107	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs12968493	0.89[CEU][hapmap]
rs12969725	0.89[CEU][hapmap]
rs13381619	0.91[CHB][hapmap]
rs1502606	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539871	0.90[JPT][hapmap]
rs1539872	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs1573363	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs1613672	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1623734	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1625400	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1627974	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap]
rs17741998	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs1787176	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1787180	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1787183	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1787185	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1787186	0.92[CEU][hapmap]
rs1787189	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1787190	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1787193	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1787194	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1792655	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1792659	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1792663	0.82[EUR][1000 genomes]
rs1792664	0.82[EUR][1000 genomes]
rs1792665	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792668	0.89[CEU][hapmap]
rs1792669	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1792670	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1792671	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1792674	0.92[CEU][hapmap]
rs1792675	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1792676	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792677	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792679	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1792680	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1792681	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792682	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1792683	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs1792686	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs1792687	0.92[CEU][hapmap]
rs1792688	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1847173	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2000708	0.80[CEU][hapmap]
rs2000709	0.91[JPT][hapmap]
rs2012555	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2047778	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096932	0.82[JPT][hapmap]
rs2096933	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs2852972	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813068	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs4940102	0.89[CEU][hapmap]
rs4940109	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs4940110	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs6507790	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs6507791	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs7228393	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7231538	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7233129	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs7236177	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs729112	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs747952	0.93[CEU][hapmap]
rs747953	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs765213	0.88[CHB][hapmap]
rs8095519	0.82[CEU][hapmap]
rs8097580	0.92[CEU][hapmap]
rs8097912	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs8099127	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs948602	0.89[CEU][hapmap]
rs948603	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs948604	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs9946556	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9955626	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs9966964	0.89[CEU][hapmap];0.90[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	esv3425854	chr18:45188942-45336590	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12454094	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45326400-45342400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr18:45327400-45358400	Weak transcription	HSMMtube	muscle
3	chr18:45327600-45352600	Weak transcription	Fetal Brain Female	brain
4	chr18:45328600-45351600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr18:45329400-45342000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr18:45332200-45342200	Weak transcription	Primary T cells from cord blood	blood
7	chr18:45332200-45352400	Weak transcription	Adipose Nuclei	Adipose
8	chr18:45332600-45351800	Weak transcription	Fetal Muscle Leg	muscle
9	chr18:45332800-45351600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr18:45333000-45357200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr18:45333200-45345600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:45333800-45351600	Weak transcription	A549	lung
13	chr18:45334600-45349800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr18:45335400-45365600	Weak transcription	Gastric	stomach
15	chr18:45335600-45336800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr18:45335600-45343600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:45335800-45336600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr18:45335800-45336800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:45335800-45351600	Weak transcription	Fetal Thymus	thymus
20	chr18:45336000-45341000	Weak transcription	Ovary	ovary
21	chr18:45336400-45336600	Enhancers	Thymus	Thymus
22	chr18:45336400-45351600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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