Variant report

Variant	rs3768227
Chromosome Location	chr1:85804087-85804088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1001604	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10489513	0.85[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs11161606	0.89[CEU][hapmap]
rs11161607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11161610	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11161611	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044537	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs12047422	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12124170	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12125557	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140103	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498375	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554597	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs173026	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs18582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884139	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2011825	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012683	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2076699	1.00[YRI][hapmap]
rs2177461	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207368	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300637	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233050	0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs233053	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes]
rs233054	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233055	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233057	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233058	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233059	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233060	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233061	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233062	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233066	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233067	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233068	0.91[EUR][1000 genomes]
rs233069	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233071	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233072	0.89[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs233074	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233091	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233095	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233097	0.92[EUR][1000 genomes]
rs233099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233108	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233109	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233112	0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233114	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233115	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233118	0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233120	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233121	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233124	0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233130	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233131	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233132	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233133	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2474123	0.82[CEU][hapmap];0.84[MEX][hapmap]
rs2892888	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3087894	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3949301	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs423105	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949890	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576763	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs6576764	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6576765	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs6576767	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657732	0.83[GIH][hapmap]
rs6657817	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6671599	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66811655	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6697083	0.91[CEU][hapmap]
rs6704103	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67611930	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72724606	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs761601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997251	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3768227	WDR63	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85792200-85806000	Weak transcription	Fetal Kidney	kidney
2	chr1:85796600-85809400	Weak transcription	Stomach Mucosa	stomach
3	chr1:85796800-85804200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:85796800-85805400	Weak transcription	Aorta	Aorta
5	chr1:85796800-85805400	Weak transcription	HepG2	liver
6	chr1:85796800-85806400	Weak transcription	Small Intestine	intestine
7	chr1:85796800-85809600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:85797000-85805000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:85798400-85804200	Weak transcription	Right Ventricle	heart
10	chr1:85798400-85806200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:85798800-85808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:85798800-85808400	Weak transcription	Ovary	ovary
13	chr1:85798800-85824800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:85798800-85824800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:85799000-85813600	Weak transcription	Fetal Intestine Large	intestine
16	chr1:85800200-85805600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:85800200-85805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:85800400-85805000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:85800400-85805400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:85800400-85808800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:85800400-85815000	Weak transcription	Fetal Intestine Small	intestine
22	chr1:85800800-85807600	Weak transcription	HSMMtube	muscle
23	chr1:85801000-85804400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:85801000-85804800	Weak transcription	HMEC	breast
25	chr1:85801600-85804400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:85802800-85804200	Strong transcription	HSMM	muscle
27	chr1:85803400-85807000	Enhancers	Hela-S3	cervix
28	chr1:85803600-85804200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:85803600-85804200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:85803600-85804200	Weak transcription	Pancreas	Pancrea
31	chr1:85803600-85804400	Enhancers	Psoas Muscle	Psoas
32	chr1:85803600-85805400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:85803600-85806800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr1:85803600-85807200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85803600-85807800	Genic enhancers	Osteobl	bone
36	chr1:85803600-85808600	Enhancers	HUVEC	blood vessel
37	chr1:85803800-85804400	Enhancers	NHLF	lung
38	chr1:85803800-85805000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:85803800-85805000	Weak transcription	NHDF-Ad	bronchial
40	chr1:85803800-85805400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:85804000-85804200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr1:85804000-85804400	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr1:85804000-85804400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:85804000-85805200	Enhancers	NH-A	brain

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