Variant report

Variant	rs11082639
Chromosome Location	chr18:45426635-45426636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr18:45426532-45426991	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:45423054..45427118-chr18:45456865..45459520,4	MCF-7	breast:
2	chr18:45425101..45428042-chr18:45452196..45454277,2	MCF-7	breast:
3	chr18:45424599..45427357-chr18:45454563..45456845,2	K562	blood:
4	chr18:45422809..45427886-chr18:45455832..45459212,8	MCF-7	breast:

Variant related genes	Relation type
SMAD2	TF binding region
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10432199	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10502890	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10853560	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11082638	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11082641	0.96[CEU][hapmap]
rs11874858	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12457664	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs12458238	0.86[CEU][hapmap]
rs12604337	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12605333	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956483	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12968107	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12968493	0.89[CEU][hapmap]
rs12969725	0.89[CEU][hapmap]
rs13381619	0.91[CHB][hapmap];0.98[ASN][1000 genomes]
rs1539872	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1573362	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs1573363	0.90[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1613672	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1631576	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17741998	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1787176	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787185	0.83[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1787186	0.84[CEU][hapmap]
rs1787193	0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787194	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787195	0.82[AMR][1000 genomes]
rs1787196	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787197	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1792653	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1792655	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1792668	0.89[CEU][hapmap]
rs1792669	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792670	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792671	0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792672	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1792674	0.85[CEU][hapmap]
rs1792675	0.86[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1792679	0.83[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792681	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs1792682	0.83[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792683	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792686	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1792687	0.85[CEU][hapmap]
rs1981	0.85[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2000708	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2000709	0.93[CEU][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2012555	0.93[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096932	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096933	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28548478	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3813068	0.89[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4939672	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4940102	0.86[CEU][hapmap]
rs4940109	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4940110	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4940120	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4940127	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61513611	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62086544	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6507790	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6507791	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs7228393	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231538	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232764	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7232893	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233129	0.90[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236177	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7237544	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7243502	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729112	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747952	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747953	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765213	0.93[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8084915	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095519	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097580	0.92[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097912	0.90[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8097925	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8099127	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099681	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs948600	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs948601	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948602	0.86[CEU][hapmap]
rs948603	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948604	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946556	0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9947494	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9950207	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9955626	0.90[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9961652	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9966637	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9966964	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

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	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11082639	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45397000-45430600	Weak transcription	Brain Angular Gyrus	brain
2	chr18:45400400-45432200	Weak transcription	Ovary	ovary
3	chr18:45410800-45428000	Weak transcription	Aorta	Aorta
4	chr18:45418200-45428400	Weak transcription	Thymus	Thymus
5	chr18:45419600-45428000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr18:45420600-45427000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr18:45420800-45433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr18:45421000-45430600	Weak transcription	Right Ventricle	heart
10	chr18:45421200-45436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr18:45421800-45428000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr18:45421800-45428400	Weak transcription	Psoas Muscle	Psoas
13	chr18:45421800-45430400	Weak transcription	Esophagus	oesophagus
14	chr18:45421800-45430600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr18:45421800-45437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr18:45422200-45429200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr18:45422200-45430600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr18:45423000-45430600	Weak transcription	NHLF	lung
19	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr18:45423200-45427600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr18:45423200-45428000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr18:45423200-45428000	Weak transcription	Fetal Thymus	thymus
23	chr18:45423200-45428000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:45423200-45428400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr18:45423200-45428400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr18:45423200-45428400	Weak transcription	Spleen	Spleen
27	chr18:45423200-45429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:45423200-45429200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr18:45423200-45429200	Weak transcription	Right Atrium	heart
30	chr18:45423200-45429200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr18:45423200-45430000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:45423200-45430600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr18:45423200-45430600	Weak transcription	Left Ventricle	heart
34	chr18:45423200-45430600	Weak transcription	Lung	lung
35	chr18:45423200-45430600	Weak transcription	Pancreas	Pancrea
36	chr18:45423200-45430600	Weak transcription	HSMM	muscle
37	chr18:45423200-45432800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr18:45423200-45438200	Weak transcription	Gastric	stomach
39	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr18:45423400-45427600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr18:45423400-45427600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr18:45423400-45428400	Weak transcription	Fetal Intestine Large	intestine
43	chr18:45423400-45428400	Weak transcription	Placenta	Placenta
44	chr18:45423600-45427600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr18:45423800-45427600	Enhancers	Primary T cells from cord blood	blood
46	chr18:45424600-45426800	Enhancers	Small Intestine	intestine
47	chr18:45424600-45426800	Enhancers	Stomach Mucosa	stomach
48	chr18:45424600-45427200	Weak transcription	Dnd41	blood
49	chr18:45424600-45431600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr18:45424800-45431000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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