Variant report

Variant	rs6507790
Chromosome Location	chr18:45431781-45431782
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:45430307..45432064-chr18:45455975..45458645,2	MCF-7	breast:
2	chr18:45429095..45432024-chr18:45444733..45448383,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10432199	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10502890	0.92[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10853560	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11082638	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]
rs11082639	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]
rs11082641	0.96[CEU][hapmap]
rs11874858	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12457664	0.92[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs12458238	0.89[CEU][hapmap]
rs12604337	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12605333	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12956483	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12968107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12968493	0.89[CEU][hapmap]
rs12969725	0.89[CEU][hapmap]
rs13381619	0.88[ASN][1000 genomes]
rs1539871	0.89[GIH][hapmap];0.84[MEX][hapmap]
rs1539872	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1573362	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1573363	0.93[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1613672	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1631576	0.94[ASW][hapmap];0.89[CEU][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17741998	0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1787176	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1787185	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1787186	0.84[CEU][hapmap]
rs1787193	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787194	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1787195	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1787196	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787197	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1792653	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792655	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1792668	0.89[CEU][hapmap]
rs1792669	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792670	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792671	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1792672	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1792674	0.85[CEU][hapmap]
rs1792675	0.89[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1792679	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1792681	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs1792682	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1792683	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1792686	0.88[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs1792687	0.85[CEU][hapmap]
rs1981	0.85[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs2000708	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000709	0.92[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2012555	0.93[CEU][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2096932	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096933	0.96[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];1.00[ASN][1000 genomes]
rs28548478	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3813068	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]
rs4939672	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4940102	0.89[CEU][hapmap]
rs4940109	0.96[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4940110	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4940120	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4940127	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61513611	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62086544	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6507791	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7228393	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7231538	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7232764	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7232893	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233129	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7236177	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237544	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243502	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729112	0.84[ASW][hapmap];0.93[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs747952	0.93[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747953	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs765213	0.92[CEU][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8084915	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8095519	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097580	0.95[CEU][hapmap];0.90[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8097912	0.93[CEU][hapmap];0.81[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8097925	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099127	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8099681	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs948600	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948601	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948602	0.89[CEU][hapmap]
rs948603	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948604	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9946556	0.89[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9947494	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9950207	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9955626	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961652	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9966637	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9966964	0.89[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[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
rs6507790	SMAD2	cis	multi-tissue	Pritchard

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45400400-45432200	Weak transcription	Ovary	ovary
2	chr18:45420800-45433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr18:45421200-45436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr18:45421800-45437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr18:45423200-45432800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr18:45423200-45438200	Weak transcription	Gastric	stomach
9	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr18:45424800-45433000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr18:45425400-45432600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr18:45425800-45432800	Weak transcription	HMEC	breast
13	chr18:45426000-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr18:45426200-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr18:45426200-45438200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr18:45426400-45432800	Weak transcription	HepG2	liver
17	chr18:45426600-45433000	Weak transcription	NHEK	skin
18	chr18:45427600-45434200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr18:45428400-45433000	Weak transcription	Fetal Kidney	kidney
20	chr18:45428600-45432600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr18:45428600-45432800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr18:45428600-45438000	Weak transcription	K562	blood
23	chr18:45429000-45433800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr18:45429400-45433000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr18:45429400-45434000	ZNF genes & repeats	A549	lung
26	chr18:45429600-45432200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr18:45429600-45432600	Weak transcription	Hela-S3	cervix
28	chr18:45429600-45432800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr18:45429600-45437800	Weak transcription	Right Atrium	heart
30	chr18:45429800-45432200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr18:45429800-45433000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr18:45429800-45435000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr18:45429800-45435800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr18:45429800-45438200	Weak transcription	Psoas Muscle	Psoas
35	chr18:45430400-45433400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr18:45430600-45431800	Enhancers	Brain Hippocampus Middle	brain
37	chr18:45430600-45432400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr18:45430600-45432800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr18:45430600-45438200	Weak transcription	Esophagus	oesophagus
40	chr18:45430800-45432000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr18:45430800-45432200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr18:45430800-45433000	Weak transcription	Brain Substantia Nigra	brain
43	chr18:45430800-45435000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr18:45430800-45435200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr18:45430800-45438400	Weak transcription	Aorta	Aorta
46	chr18:45431000-45431800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr18:45431000-45432000	Weak transcription	Thymus	Thymus
48	chr18:45431000-45432000	Weak transcription	Spleen	Spleen
49	chr18:45431000-45432200	Weak transcription	Fetal Thymus	thymus
50	chr18:45431000-45432200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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