Variant report

Variant	rs9988451
Chromosome Location	chr1:45340282-45340283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10158188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10465818	0.87[ASW][hapmap]
rs11211031	0.87[ASW][hapmap]
rs11211037	0.96[CEU][hapmap];0.92[TSI][hapmap]
rs11211044	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211047	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11573543	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs11577974	0.84[CEU][hapmap]
rs11584031	0.96[CEU][hapmap]
rs12059964	0.87[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.82[ASN][1000 genomes]
rs12094007	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12118515	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120470	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144803	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1226572	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs12408818	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12568071	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12568279	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273940	0.89[EUR][1000 genomes]
rs263956	0.84[ASN][1000 genomes]
rs263962	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs263965	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs263966	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs263975	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263977	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs263980	0.83[ASN][1000 genomes]
rs263987	0.84[ASN][1000 genomes]
rs263990	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap]
rs264005	0.82[ASN][1000 genomes]
rs264009	0.83[ASN][1000 genomes]
rs264011	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs264014	0.86[JPT][hapmap]
rs2983715	0.82[JPT][hapmap]
rs3121173	0.83[ASN][1000 genomes]
rs36107413	0.83[ASN][1000 genomes]
rs3795720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs438493	0.83[ASN][1000 genomes]
rs452989	0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs6429548	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs6688465	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696675	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6698951	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514741	0.88[EUR][1000 genomes]
rs7524446	0.81[CHB][hapmap]
rs7525308	0.87[ASW][hapmap];0.96[CEU][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs7526786	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7545808	0.89[EUR][1000 genomes]
rs7554177	0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs932691	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429058	0.83[ASN][1000 genomes]
rs9645347	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
2	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
3	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
4	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45308800-45345400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:45309200-45343000	Weak transcription	Esophagus	oesophagus
3	chr1:45309200-45345200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:45309200-45360600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:45309400-45340400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:45309400-45343000	Weak transcription	Colonic Mucosa	Colon
7	chr1:45309400-45350400	Weak transcription	HUVEC	blood vessel
8	chr1:45309600-45343000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:45309600-45352400	Weak transcription	Fetal Heart	heart
10	chr1:45309600-45354200	Weak transcription	Fetal Brain Male	brain
11	chr1:45313400-45343600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:45313400-45360200	Weak transcription	Hela-S3	cervix
13	chr1:45314600-45349000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:45315000-45341000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:45315000-45349000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:45315200-45345000	Weak transcription	Right Ventricle	heart
17	chr1:45315600-45343000	Weak transcription	Brain Substantia Nigra	brain
18	chr1:45316000-45341000	Weak transcription	Thymus	Thymus
19	chr1:45316000-45349000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:45316600-45351800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:45316800-45340400	Weak transcription	Fetal Lung	lung
22	chr1:45316800-45340600	Weak transcription	Lung	lung
23	chr1:45317800-45355600	Weak transcription	NHDF-Ad	bronchial
24	chr1:45320000-45348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:45322000-45350400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:45322600-45360000	Weak transcription	Small Intestine	intestine
27	chr1:45322800-45343400	Weak transcription	Brain Germinal Matrix	brain
28	chr1:45325000-45341000	Weak transcription	Pancreas	Pancrea
29	chr1:45326000-45346600	Weak transcription	HMEC	breast
30	chr1:45326600-45343600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:45326800-45349000	Weak transcription	GM12878-XiMat	blood
32	chr1:45326800-45350400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:45327000-45341400	Strong transcription	Liver	Liver
34	chr1:45327200-45341000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:45327800-45343400	Weak transcription	HSMMtube	muscle
36	chr1:45327800-45350000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:45328800-45340600	Weak transcription	Placenta	Placenta
38	chr1:45329200-45341000	Weak transcription	NHEK	skin
39	chr1:45331200-45352200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr1:45331600-45352400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:45332000-45341400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:45332000-45341400	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:45332000-45345000	Weak transcription	A549	lung
44	chr1:45332400-45341400	Strong transcription	Primary T cells from cord blood	blood
45	chr1:45332400-45341400	Strong transcription	Adipose Nuclei	Adipose
46	chr1:45332400-45341400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:45332400-45341400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:45332600-45357200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:45333200-45340400	Weak transcription	Aorta	Aorta
50	chr1:45333200-45343000	Weak transcription	Spleen	Spleen

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