Variant report

Variant	rs4654017
Chromosome Location	chr1:224473294-224473295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10158063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10733024	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737442	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10737443	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10753462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10753464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799556	1.00[MEX][hapmap]
rs10799562	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799563	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10799566	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799567	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10799568	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916577	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10916585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11802486	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11811730	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846214	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1806742	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2001712	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2001713	1.00[EUR][1000 genomes]
rs2404783	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404856	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2404857	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2404858	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404859	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2405062	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405067	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405070	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2896990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2896992	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2897054	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767722	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767723	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3767724	0.95[ASN][1000 genomes]
rs3767725	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4146965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4146966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4233234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4233235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs4256779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4420060	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4457542	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4628473	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653575	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653581	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653583	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4653584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4654011	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4654013	0.85[JPT][hapmap]
rs4654019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654022	0.89[CHB][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4654032	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4654033	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4654034	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55675086	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55980628	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57324770	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58855990	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59106681	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426088	0.89[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs6426094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6426110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6426114	0.88[ASN][1000 genomes]
rs6426115	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426117	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6682667	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685600	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691689	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6696795	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6699017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73118046	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73128468	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130436	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130448	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130455	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130462	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73130464	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521015	0.80[ASW][hapmap];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];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529143	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530205	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7534101	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7534447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9287027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4654017	NVL	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
2	chr1:224412400-224473600	Weak transcription	HepG2	liver
3	chr1:224424600-224479600	Weak transcription	Pancreas	Pancrea
4	chr1:224431200-224490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:224433400-224516200	Weak transcription	Fetal Heart	heart
6	chr1:224434400-224474800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:224434400-224474800	Weak transcription	Fetal Brain Male	brain
8	chr1:224436800-224473600	Weak transcription	Gastric	stomach
9	chr1:224437000-224475200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:224437000-224476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:224437000-224479600	Weak transcription	Right Ventricle	heart
12	chr1:224437600-224474800	Weak transcription	Colonic Mucosa	Colon
13	chr1:224438000-224474600	Weak transcription	Brain Angular Gyrus	brain
14	chr1:224439800-224501600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:224440400-224474800	Weak transcription	Fetal Kidney	kidney
16	chr1:224444600-224479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:224445400-224482000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:224450600-224473600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:224450800-224480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:224454800-224475400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:224454800-224480000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:224455000-224474800	Weak transcription	Ovary	ovary
23	chr1:224455000-224480200	Weak transcription	Psoas Muscle	Psoas
24	chr1:224456000-224474600	Weak transcription	Brain Anterior Caudate	brain
25	chr1:224457200-224479600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:224461200-224505600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:224461600-224475400	Weak transcription	Lung	lung
28	chr1:224462000-224473800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:224462200-224479600	Weak transcription	Spleen	Spleen
30	chr1:224463000-224473600	Weak transcription	NHLF	lung
31	chr1:224463200-224473600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:224463200-224473600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:224463200-224473600	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:224463200-224473600	Weak transcription	Fetal Lung	lung
35	chr1:224463200-224473600	Weak transcription	Left Ventricle	heart
36	chr1:224463200-224474800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:224463200-224474800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:224463200-224474800	Weak transcription	Brain Substantia Nigra	brain
39	chr1:224463200-224474800	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:224463400-224474200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:224463800-224474400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:224464000-224475200	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:224464800-224474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:224464800-224474800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:224465000-224487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:224465000-224488000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:224465000-224504400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:224465000-224504400	Strong transcription	Liver	Liver
49	chr1:224465000-224505200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:224465000-224505600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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