Variant report

Variant	rs11082638
Chromosome Location	chr18:45421899-45421900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45412259..45415200-chr18:45419567..45423866,3	MCF-7	breast:
2	chr18:45419311..45422107-chr18:45455091..45458226,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB7C-5	chr18:45421638-45422096	NONHSAT059175

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10432199	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10502890	0.85[CEU][hapmap]
rs10853560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11082639	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	0.89[CEU][hapmap]
rs11874858	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12457664	0.85[CEU][hapmap]
rs12458238	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12604337	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12605333	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956483	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12968107	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12968493	0.96[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12969725	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13381619	0.91[CHB][hapmap];0.98[ASN][1000 genomes]
rs1539871	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs1539872	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1573362	0.85[CEU][hapmap]
rs1573363	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1613672	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17741998	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1787176	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787185	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1787186	0.92[CEU][hapmap]
rs1787193	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787195	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787196	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787197	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1787198	0.84[EUR][1000 genomes]
rs1792653	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792667	0.84[EUR][1000 genomes]
rs1792668	0.96[CEU][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs1792669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792671	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792672	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792674	0.92[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1792675	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792679	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792681	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs1792682	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1792683	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792686	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs1792687	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1981	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2000708	0.89[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2000709	0.85[CEU][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2012555	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096932	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096933	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28548478	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35710478	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3813068	0.83[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4939672	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4940102	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4940109	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4940110	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4940120	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4940127	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61513611	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62086544	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6507790	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6507791	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs7228393	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232764	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7232893	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233129	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236177	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7237544	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7243502	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729112	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747952	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765213	0.85[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8084915	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095519	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097580	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097912	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8097925	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8099127	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099681	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs948600	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs948601	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948602	0.96[CEU][hapmap]
rs948603	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948604	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946556	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9947494	0.83[ASN][1000 genomes]
rs9950207	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9955626	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9966637	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9966964	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11082638	SMAD2	Cis_1M	lymphoblastoid	RTeQTL
rs11082638	SMAD2	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45384200-45423000	Weak transcription	Lung	lung
2	chr18:45384400-45423000	Weak transcription	Spleen	Spleen
3	chr18:45397000-45430600	Weak transcription	Brain Angular Gyrus	brain
4	chr18:45400400-45432200	Weak transcription	Ovary	ovary
5	chr18:45400600-45424600	Weak transcription	Stomach Mucosa	stomach
6	chr18:45401200-45426000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr18:45401400-45424600	Weak transcription	Brain Hippocampus Middle	brain
8	chr18:45401600-45423400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr18:45403800-45422200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr18:45405200-45423400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr18:45408800-45423000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:45409200-45426400	Weak transcription	Fetal Kidney	kidney
13	chr18:45410600-45425000	Weak transcription	HSMMtube	muscle
14	chr18:45410800-45422800	Weak transcription	NHLF	lung
15	chr18:45410800-45424400	Weak transcription	Colon Smooth Muscle	Colon
16	chr18:45410800-45424400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr18:45410800-45424600	Weak transcription	Brain Substantia Nigra	brain
18	chr18:45410800-45424800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr18:45410800-45425800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr18:45410800-45428000	Weak transcription	Aorta	Aorta
21	chr18:45411800-45424600	Strong transcription	Dnd41	blood
22	chr18:45412400-45422000	Weak transcription	Fetal Intestine Small	intestine
23	chr18:45414000-45422800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr18:45415200-45423000	Strong transcription	Fetal Thymus	thymus
25	chr18:45415200-45426000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr18:45415800-45423800	Weak transcription	NHDF-Ad	bronchial
27	chr18:45415800-45425200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr18:45417200-45424200	Weak transcription	NH-A	brain
29	chr18:45417400-45426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr18:45418000-45422200	Weak transcription	Fetal Lung	lung
31	chr18:45418000-45423200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr18:45418000-45424600	Weak transcription	Liver	Liver
33	chr18:45418200-45422800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr18:45418200-45428400	Weak transcription	Thymus	Thymus
35	chr18:45419000-45423400	Strong transcription	Primary B cells from cord blood	blood
36	chr18:45419600-45423000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr18:45419600-45423200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr18:45419600-45423200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:45419600-45428000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr18:45420000-45426200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr18:45420200-45422200	Strong transcription	GM12878-XiMat	blood
42	chr18:45420200-45423200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:45420400-45422000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr18:45420400-45422000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr18:45420400-45422200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr18:45420400-45422200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr18:45420400-45422200	Strong transcription	HepG2	liver
48	chr18:45420400-45422800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr18:45420400-45423200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr18:45420400-45423200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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