Variant report

Variant	rs12968107
Chromosome Location	chr18:45432593-45432594
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	chr18:45428185..45429886-chr18:45431869..45434765,2	K562	blood:
2	chr18:45431906..45433544-chr18:45439768..45441940,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10432199	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10502890	0.85[CEU][hapmap]
rs10853560	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11082638	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]
rs11082639	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11082641	0.86[CEU][hapmap]
rs11874858	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12457664	0.85[CEU][hapmap]
rs12458238	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12604337	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12605333	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12956483	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12968493	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12969725	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs13381619	0.88[ASN][1000 genomes]
rs1539872	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1573362	0.82[CEU][hapmap]
rs1573363	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1613672	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17741998	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1787176	0.96[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1787185	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs1787186	0.91[CEU][hapmap]
rs1787193	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1787195	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787196	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787197	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1787198	0.83[EUR][1000 genomes]
rs1792653	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792667	0.83[EUR][1000 genomes]
rs1792668	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1792669	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792670	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792671	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs1792672	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1792674	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1792675	0.96[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792679	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs1792681	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1792682	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs1792683	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1792686	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs1792687	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs1981	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs2000708	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000709	0.82[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2012555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2096932	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096933	0.86[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]
rs28548478	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35710478	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3813068	0.96[CEU][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4939672	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4940102	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs4940109	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4940110	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4940120	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4940127	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61513611	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62086544	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6507790	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]
rs6507791	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7228393	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7231538	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7232764	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7232893	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233129	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7236177	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]
rs7237544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243502	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729112	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs747952	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs747953	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs765213	0.82[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8084915	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8095519	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8097580	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8097912	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8097925	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099127	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8099681	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs948600	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948601	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948602	0.96[CEU][hapmap]
rs948603	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs948604	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9946556	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9950207	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9955626	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9966637	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9966964	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.95[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
rs12968107	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45420800-45433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr18:45421200-45436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:45421800-45437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr18:45423200-45432800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr18:45423200-45438200	Weak transcription	Gastric	stomach
8	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr18:45424800-45433000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr18:45425400-45432600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr18:45425800-45432800	Weak transcription	HMEC	breast
12	chr18:45426000-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:45426200-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:45426200-45438200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr18:45426400-45432800	Weak transcription	HepG2	liver
16	chr18:45426600-45433000	Weak transcription	NHEK	skin
17	chr18:45427600-45434200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr18:45428400-45433000	Weak transcription	Fetal Kidney	kidney
19	chr18:45428600-45432600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr18:45428600-45432800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr18:45428600-45438000	Weak transcription	K562	blood
22	chr18:45429000-45433800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr18:45429400-45433000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr18:45429400-45434000	ZNF genes & repeats	A549	lung
25	chr18:45429600-45432600	Weak transcription	Hela-S3	cervix
26	chr18:45429600-45432800	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:45429600-45437800	Weak transcription	Right Atrium	heart
28	chr18:45429800-45433000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr18:45429800-45435000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr18:45429800-45435800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr18:45429800-45438200	Weak transcription	Psoas Muscle	Psoas
32	chr18:45430400-45433400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr18:45430600-45432800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr18:45430600-45438200	Weak transcription	Esophagus	oesophagus
35	chr18:45430800-45433000	Weak transcription	Brain Substantia Nigra	brain
36	chr18:45430800-45435000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr18:45430800-45435200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr18:45430800-45438400	Weak transcription	Aorta	Aorta
39	chr18:45431000-45432600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr18:45431000-45432600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr18:45431000-45432800	Weak transcription	Fetal Brain Male	brain
42	chr18:45431000-45432800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr18:45431000-45433000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr18:45431000-45433000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr18:45431000-45433000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr18:45431000-45433000	Weak transcription	Brain Angular Gyrus	brain
47	chr18:45431000-45433000	Weak transcription	Pancreas	Pancrea
48	chr18:45431000-45434600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr18:45431000-45437800	Weak transcription	Left Ventricle	heart
50	chr18:45431000-45438000	Weak transcription	Fetal Heart	heart

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