Variant report

Variant	rs371076
Chromosome Location	chr1:78122501-78122502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1038983	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10782654	0.81[ASN][1000 genomes]
rs10873949	0.81[ASN][1000 genomes]
rs10873950	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs10873951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10873955	0.94[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs11162362	0.81[ASN][1000 genomes]
rs11162364	0.82[ASN][1000 genomes]
rs11162365	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11162366	0.87[EUR][1000 genomes]
rs11162369	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162372	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11162378	0.83[GIH][hapmap]
rs11162380	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11162386	0.94[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs11162387	0.87[CEU][hapmap]
rs11578805	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1166584	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1166586	0.82[CEU][hapmap]
rs1166588	0.83[ASW][hapmap];0.83[CEU][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs12026939	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12074409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12128041	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12142671	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12717767	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12724560	0.81[ASN][1000 genomes]
rs1389789	0.83[GIH][hapmap]
rs1389790	0.81[GIH][hapmap]
rs1565850	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1565851	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1565852	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1962523	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1977900	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2029768	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.81[ASN][1000 genomes]
rs203229	0.83[GIH][hapmap]
rs2147318	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs2274123	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2647486	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs278833	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278836	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs278837	0.83[GIH][hapmap]
rs278838	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278842	0.83[GIH][hapmap]
rs278843	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278845	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278847	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278850	0.83[GIH][hapmap]
rs278852	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278854	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278857	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278858	0.94[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs278859	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278862	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs278864	0.89[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2803136	0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2803168	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs3509	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs366467	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs370335	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3767030	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap]
rs3767037	0.83[GIH][hapmap]
rs4245658	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4589153	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4600093	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949658	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949659	0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4949661	0.89[EUR][1000 genomes]
rs4949808	0.81[ASN][1000 genomes]
rs4949809	1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4949811	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs4949813	0.85[ASN][1000 genomes]
rs4949814	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs4949816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4949818	0.83[GIH][hapmap]
rs4949822	0.80[AMR][1000 genomes]
rs574973	0.83[GIH][hapmap]
rs6603955	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6603956	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6657290	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6661656	0.81[GIH][hapmap]
rs6667519	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6667803	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6670660	0.89[EUR][1000 genomes]
rs6672200	0.94[CEU][hapmap];0.80[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6674638	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6675743	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs6687501	0.83[GIH][hapmap]
rs6691317	0.88[EUR][1000 genomes]
rs6692369	0.81[ASN][1000 genomes]
rs6693100	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6695989	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6696083	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6698151	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6699311	0.81[GIH][hapmap]
rs728741	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs7513619	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7519476	0.81[ASN][1000 genomes]
rs7521042	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7524147	0.81[ASN][1000 genomes]
rs7524866	0.93[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7531286	0.89[CHB][hapmap]
rs7545175	0.89[EUR][1000 genomes]
rs7545544	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7546365	0.80[GIH][hapmap]
rs7551211	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7551729	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs7552291	0.94[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs872342	0.83[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs962388	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9662527	0.94[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv830303	chr1:78090824-78308765	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs371076	USP33	Cis_1M	lymphoblastoid	RTeQTL
rs371076	AK5	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78099000-78147200	Weak transcription	Gastric	stomach
2	chr1:78099200-78132400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:78100800-78133200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:78105200-78131800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:78107600-78146000	Weak transcription	Fetal Kidney	kidney
6	chr1:78110400-78138000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:78111200-78125600	Weak transcription	HSMM	muscle
8	chr1:78111200-78147200	Weak transcription	Esophagus	oesophagus
9	chr1:78111400-78123200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:78111400-78125400	Weak transcription	Left Ventricle	heart
11	chr1:78111400-78127200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:78111400-78128000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:78111400-78130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:78111400-78137400	Weak transcription	HUVEC	blood vessel
15	chr1:78111400-78137600	Weak transcription	Hela-S3	cervix
16	chr1:78112200-78139000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:78114800-78135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:78114800-78135800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:78116800-78144600	Weak transcription	NHEK	skin
20	chr1:78117000-78122800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr1:78117000-78124000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:78117000-78128200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:78117000-78128200	Weak transcription	Fetal Stomach	stomach
24	chr1:78117000-78130000	Weak transcription	Fetal Lung	lung
25	chr1:78117000-78130600	Weak transcription	Liver	Liver
26	chr1:78117000-78130600	Weak transcription	Brain Angular Gyrus	brain
27	chr1:78117000-78130800	Weak transcription	K562	blood
28	chr1:78117200-78144400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:78117400-78122800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:78117400-78123000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:78117400-78134800	Weak transcription	Osteobl	bone
32	chr1:78117400-78137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:78117400-78138000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:78117400-78141800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:78117400-78147200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:78117600-78123600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:78117600-78137400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:78117600-78137600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:78117600-78138200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:78117600-78139800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:78117600-78146000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:78117600-78147200	Weak transcription	Thymus	Thymus
43	chr1:78118200-78123000	Weak transcription	Primary B cells from cord blood	blood
44	chr1:78118200-78137200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:78118600-78130800	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:78118600-78146000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr1:78118800-78130600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:78119000-78122600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:78119000-78122600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:78119000-78126200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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