Variant report

Variant	rs1792682
Chromosome Location	chr18:45373727-45373728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45372242..45375198-chr18:45455382..45457471,2	K562	blood:
2	chr18:45367507..45370509-chr18:45371769..45374946,4	K562	blood:
3	chr18:45368468..45370509-chr18:45372236..45375671,3	K562	blood:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10853560	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11082638	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11082639	0.83[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11082641	0.80[CEU][hapmap]
rs12454094	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12455876	0.81[EUR][1000 genomes]
rs12458238	0.89[CEU][hapmap]
rs12956483	0.84[EUR][1000 genomes]
rs12968107	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs12968493	0.89[CEU][hapmap]
rs12969725	0.89[CEU][hapmap]
rs13381619	1.00[CHB][hapmap]
rs1502606	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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];0.87[YRI][hapmap]
rs1613672	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs1623734	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1625400	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1627974	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs17741998	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1787176	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs1787180	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1787183	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787186	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1787189	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787190	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1787193	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1792653	0.84[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1792659	0.88[EUR][1000 genomes]
rs1792665	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792668	0.89[CEU][hapmap]
rs1792669	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792670	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792674	0.92[CEU][hapmap]
rs1792675	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1792676	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792677	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792678	0.83[EUR][1000 genomes]
rs1792679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792680	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792681	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792683	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs1792686	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792687	0.92[CEU][hapmap]
rs1792688	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847173	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2000708	0.80[CEU][hapmap]
rs2000709	0.91[JPT][hapmap]
rs2012555	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2047778	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2096932	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2096933	0.80[CEU][hapmap];0.82[JPT][hapmap]
rs2852972	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28548478	0.83[EUR][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]
rs62086544	0.84[EUR][1000 genomes]
rs6507790	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6507791	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs7228393	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7231538	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs7233129	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs7236177	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs729112	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs747952	0.93[CEU][hapmap]
rs747953	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs765213	0.94[CHB][hapmap]
rs8095519	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs8097580	0.96[CEU][hapmap];0.84[CHB][hapmap]
rs8097912	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs8099127	0.93[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs8099681	0.83[EUR][1000 genomes]
rs948602	0.89[CEU][hapmap]
rs948603	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs948604	0.82[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs9946556	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9955626	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs9966964	0.89[CEU][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	nsv1064797	chr18:45372027-45394386	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1063859	chr18:45372027-45404492	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1792682	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	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr18:45347600-45381800	Weak transcription	Right Ventricle	heart
4	chr18:45351000-45374600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr18:45353000-45381200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:45354600-45381800	Weak transcription	Fetal Intestine Small	intestine
7	chr18:45355600-45375600	Strong transcription	Hela-S3	cervix
8	chr18:45355600-45375800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr18:45355600-45376200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr18:45356000-45378000	Weak transcription	Small Intestine	intestine
11	chr18:45356200-45377800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:45356200-45384000	Weak transcription	Spleen	Spleen
13	chr18:45356600-45376200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr18:45358600-45376400	Strong transcription	Dnd41	blood
15	chr18:45358800-45382400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr18:45359000-45374400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr18:45359800-45375600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr18:45359800-45375600	Strong transcription	Fetal Thymus	thymus
19	chr18:45360000-45375400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr18:45360000-45375600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr18:45361400-45375600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr18:45361400-45375600	Strong transcription	A549	lung
23	chr18:45361400-45376000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr18:45362400-45375200	Strong transcription	Primary B cells from cord blood	blood
25	chr18:45362400-45375600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr18:45362600-45375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr18:45363000-45375800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr18:45363800-45375600	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr18:45363800-45375600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr18:45363800-45376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:45364000-45375400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr18:45364400-45375600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr18:45364600-45375600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr18:45364600-45376200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr18:45365200-45375800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr18:45365400-45375000	Strong transcription	GM12878-XiMat	blood
37	chr18:45365800-45381800	Weak transcription	Psoas Muscle	Psoas
38	chr18:45366000-45381800	Weak transcription	Aorta	Aorta
39	chr18:45366200-45390000	Weak transcription	Colonic Mucosa	Colon
40	chr18:45366400-45384000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr18:45366400-45384000	Weak transcription	Brain Angular Gyrus	brain
42	chr18:45366400-45384000	Weak transcription	Esophagus	oesophagus
43	chr18:45366600-45408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr18:45367800-45375000	Strong transcription	Fetal Muscle Trunk	muscle
45	chr18:45368000-45375400	Strong transcription	HSMM	muscle
46	chr18:45368200-45375800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr18:45368200-45384000	Weak transcription	Stomach Mucosa	stomach
48	chr18:45368400-45377200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr18:45369000-45381800	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr18:45369200-45381200	Weak transcription	Brain Germinal Matrix	brain

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