Variant report

Variant	rs1498373
Chromosome Location	chr1:85790633-85790634
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];0.82[EUR][1000 genomes]
rs11161606	0.89[CEU][hapmap]
rs11161607	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161610	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11161611	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044537	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs12047422	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12124170	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125557	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12140103	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554597	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs173026	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs18582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1884139	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2011825	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2012683	0.91[EUR][1000 genomes];0.95[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];0.92[ASN][1000 genomes]
rs2207368	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2268667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300637	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs233047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233050	0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233053	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs233054	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233055	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs233057	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233058	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233059	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233060	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233061	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233062	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233066	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233067	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233068	0.91[EUR][1000 genomes]
rs233069	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233071	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233072	0.89[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs233074	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233091	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233095	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs233108	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233109	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs233112	0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs233113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233114	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233118	0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233120	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233121	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233124	0.89[CEU][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs233127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233130	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233131	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233132	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs233133	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2474123	0.82[CEU][hapmap]
rs2892888	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3087894	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768227	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]
rs3949301	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs423105	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949890	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4949900	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576763	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs6576764	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6576765	0.85[CEU][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs6576767	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6657732	0.83[GIH][hapmap]
rs6657817	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671599	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66811655	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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];0.92[ASN][1000 genomes]
rs67611930	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72724606	0.91[EUR][1000 genomes];0.90[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];0.85[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs997251	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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
rs1498373	WDR63	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85774600-85794800	Weak transcription	Spleen	Spleen
2	chr1:85774800-85794200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:85780000-85791800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:85780000-85795800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:85780200-85795800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:85780400-85791600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:85780400-85793200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:85780400-85795800	Weak transcription	Gastric	stomach
9	chr1:85781800-85792800	Weak transcription	Pancreas	Pancrea
10	chr1:85782400-85795000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:85782800-85794600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:85783000-85795800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:85783200-85795800	Weak transcription	Aorta	Aorta
14	chr1:85783800-85791000	Genic enhancers	Osteobl	bone
15	chr1:85784000-85794600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:85784600-85794600	Weak transcription	Fetal Lung	lung
17	chr1:85786400-85791200	Strong transcription	Fetal Intestine Small	intestine
18	chr1:85786600-85791400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:85786600-85791600	Weak transcription	Fetal Kidney	kidney
20	chr1:85787200-85793600	Weak transcription	HSMMtube	muscle
21	chr1:85787400-85791600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:85787600-85790800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:85787600-85791000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:85787600-85791400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:85787600-85791400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:85788600-85797400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:85788800-85791000	Weak transcription	HMEC	breast
28	chr1:85788800-85791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:85788800-85791600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:85789000-85791000	Weak transcription	NHEK	skin
31	chr1:85789000-85791400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:85789400-85790800	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:85789400-85790800	Weak transcription	HSMM	muscle
34	chr1:85789400-85795800	Weak transcription	Liver	Liver
35	chr1:85789600-85791000	Weak transcription	HepG2	liver
36	chr1:85789600-85794600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:85789800-85790800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:85789800-85791400	Weak transcription	Fetal Intestine Large	intestine
39	chr1:85789800-85795800	Weak transcription	Fetal Stomach	stomach
40	chr1:85789800-85795800	Weak transcription	Lung	lung
41	chr1:85790000-85792000	Enhancers	Fetal Heart	heart
42	chr1:85790000-85795600	Enhancers	NHDF-Ad	bronchial
43	chr1:85790200-85791400	Enhancers	A549	lung
44	chr1:85790200-85792200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:85790200-85795200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:85790400-85790800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr1:85790400-85790800	Enhancers	NHLF	lung
48	chr1:85790400-85791000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:85790400-85791000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:85790400-85791200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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