Variant report

Variant	rs3813068
Chromosome Location	chr18:45438066-45438067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45436938..45439743-chr18:45441401..45443644,2	MCF-7	breast:
2	chr18:45436720..45439096-chr18:45454561..45459075,5	K562	blood:
3	chr18:45435138..45437489-chr18:45437508..45439751,3	MCF-7	breast:
4	chr18:45419455..45422415-chr18:45437931..45439603,2	K562	blood:
5	chr18:45436405..45438633-chr18:45455845..45457849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10432199	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10502890	0.89[CEU][hapmap]
rs10853560	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11082638	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]
rs11082639	0.89[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11082641	0.85[CEU][hapmap]
rs11874858	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12457664	0.89[CEU][hapmap]
rs12458238	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12604337	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12605333	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12956483	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12968107	0.96[CEU][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12968493	0.92[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12969725	0.92[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1539871	0.91[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs1539872	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573362	0.89[CEU][hapmap]
rs1573363	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613672	0.93[CEU][hapmap];0.82[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1631576	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17741998	0.96[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1787176	0.93[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1787185	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1787186	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs1787193	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1787194	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787195	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787196	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787197	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1787198	0.83[EUR][1000 genomes]
rs1792653	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792655	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792667	0.83[EUR][1000 genomes]
rs1792668	0.92[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1792669	0.96[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1792670	0.96[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1792671	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs1792672	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792674	0.89[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1792675	0.93[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792679	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1792681	0.85[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs1792682	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1792683	1.00[ASW][hapmap];0.85[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1792686	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs1792687	0.89[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1981	0.89[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap]
rs2000708	0.93[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2000709	0.89[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012555	0.96[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2096932	0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2096933	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28548478	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35710478	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4939672	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940102	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4940109	0.93[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4940110	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940120	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4940127	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61513611	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62086544	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6507790	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6507791	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7228393	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7231538	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7232764	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7232893	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7233129	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7236177	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7237544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7243502	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs729112	0.83[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs747952	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs747953	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs765213	0.89[CEU][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8084915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8095519	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8097580	0.95[CEU][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8097912	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097925	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8099127	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8099681	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs948600	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs948601	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs948602	0.92[CEU][hapmap]
rs948603	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs948604	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9946556	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9950207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9955626	0.96[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9961652	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9966637	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9966964	0.88[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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
rs3813068	SMAD2	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr18:45423200-45438200	Weak transcription	Gastric	stomach
3	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr18:45426200-45438200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr18:45429800-45438200	Weak transcription	Psoas Muscle	Psoas
6	chr18:45430600-45438200	Weak transcription	Esophagus	oesophagus
7	chr18:45430800-45438400	Weak transcription	Aorta	Aorta
8	chr18:45431000-45438200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:45431000-45438200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:45431000-45438200	Weak transcription	Right Ventricle	heart
11	chr18:45431000-45438400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:45431000-45442800	Weak transcription	Lung	lung
13	chr18:45431800-45438200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr18:45433200-45438200	Weak transcription	Ovary	ovary
15	chr18:45433200-45438200	Weak transcription	HMEC	breast
16	chr18:45433200-45438200	Weak transcription	NHEK	skin
17	chr18:45433200-45438600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr18:45433200-45438600	Weak transcription	Fetal Kidney	kidney
19	chr18:45433200-45439400	Weak transcription	Pancreas	Pancrea
20	chr18:45433200-45455000	Weak transcription	Fetal Stomach	stomach
21	chr18:45433200-45455400	Weak transcription	Fetal Brain Male	brain
22	chr18:45433400-45438200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr18:45433400-45438200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr18:45433400-45438200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr18:45433400-45438200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr18:45433400-45439400	Weak transcription	Stomach Mucosa	stomach
27	chr18:45433400-45439600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:45433400-45442800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:45433400-45442800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr18:45433400-45446400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:45433400-45452200	Weak transcription	Fetal Lung	lung
32	chr18:45433600-45446000	Weak transcription	Placenta	Placenta
33	chr18:45433800-45440400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr18:45434000-45438600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr18:45434000-45442000	Weak transcription	HSMM	muscle
36	chr18:45434000-45446600	Weak transcription	Primary B cells from cord blood	blood
37	chr18:45434000-45454600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr18:45434200-45438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr18:45434800-45438400	Weak transcription	A549	lung
40	chr18:45435000-45438200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr18:45435000-45442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:45435200-45438400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr18:45435200-45438400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr18:45435200-45438400	Weak transcription	Hela-S3	cervix
45	chr18:45435200-45438800	Strong transcription	Dnd41	blood
46	chr18:45435200-45439600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr18:45435400-45438200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr18:45435400-45438200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr18:45435400-45452400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr18:45435600-45438400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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