Variant report

Variant	rs2663067
Chromosome Location	chr10:50155130-50155131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1015717	0.89[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10735228	0.89[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs10745290	0.82[CEU][hapmap]
rs10776658	0.88[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10776659	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10776660	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857430	0.82[CEU][hapmap]
rs10857661	0.88[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs10857662	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11101572	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11101573	0.89[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12413832	0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1877799	0.82[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs1877800	0.89[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs1913516	0.84[CEU][hapmap]
rs2137909	0.81[CEU][hapmap]
rs2137913	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2249429	0.94[JPT][hapmap];0.82[TSI][hapmap]
rs2249657	0.81[CEU][hapmap]
rs2252811	0.94[JPT][hapmap];0.82[TSI][hapmap]
rs2255553	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2271565	0.82[CEU][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs2292584	0.82[CEU][hapmap]
rs2292585	0.82[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs2457466	0.96[CEU][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2663028	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663068	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2671715	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2889709	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3750867	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829206	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4317902	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4614357	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4838433	0.94[JPT][hapmap]
rs61848117	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6537586	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6537587	0.82[CEU][hapmap]
rs7072344	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7082322	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7083751	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7086917	0.85[CEU][hapmap]
rs7091429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7093656	0.82[CEU][hapmap];0.87[GIH][hapmap]
rs7098224	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.85[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2663067	CSTF2T	cis	parietal	SCAN
rs2663067	WDFY4	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50121000-50155800	Weak transcription	Primary T cells from cord blood	blood
2	chr10:50134600-50160400	Weak transcription	Right Atrium	heart
3	chr10:50143600-50164400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:50144600-50196200	Strong transcription	Primary B cells from cord blood	blood
5	chr10:50145000-50193200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr10:50145400-50193200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr10:50145800-50193400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr10:50148000-50193600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr10:50149600-50161200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr10:50150400-50159000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:50153000-50156200	Enhancers	Fetal Muscle Trunk	muscle
12	chr10:50153200-50156400	Enhancers	Fetal Muscle Leg	muscle
13	chr10:50153400-50187800	Strong transcription	GM12878-XiMat	blood
14	chr10:50153600-50155200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr10:50153600-50193600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr10:50153800-50155200	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr10:50154400-50159200	Strong transcription	Primary hematopoietic stem cells	blood
18	chr10:50154600-50155200	Enhancers	Stomach Mucosa	stomach
19	chr10:50154600-50155200	Strong transcription	Spleen	Spleen
20	chr10:50154600-50160400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:50154600-50162000	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:50154800-50155200	Enhancers	Esophagus	oesophagus
23	chr10:50154800-50155200	Enhancers	Fetal Lung	lung
24	chr10:50154800-50155200	Enhancers	Ovary	ovary
25	chr10:50154800-50155200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr10:50154800-50155800	Enhancers	Lung	lung
27	chr10:50154800-50165800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr10:50155000-50155200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:50155000-50155200	Flanking Active TSS	HUVEC	blood vessel
30	chr10:50155000-50155800	Enhancers	Gastric	stomach
31	chr10:50155000-50156400	Enhancers	Fetal Stomach	stomach
32	chr10:50155000-50160000	Weak transcription	Aorta	Aorta

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