Variant report

Variant	rs10483649
Chromosome Location	chr14:56108007-56108008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10136408	0.85[CEU][hapmap]
rs10146870	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs10444721	0.81[JPT][hapmap]
rs10483644	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12432344	0.84[EUR][1000 genomes]
rs12432588	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12432887	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12433592	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12434609	0.80[ASN][1000 genomes]
rs12434624	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12434660	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12434799	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12435643	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12587700	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12587705	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12587735	0.81[JPT][hapmap];0.81[TSI][hapmap]
rs12588185	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12589864	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12589867	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12590388	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12590936	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12882850	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12885864	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12888809	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12891489	0.85[CEU][hapmap]
rs12891526	0.84[ASN][1000 genomes]
rs12893162	0.93[ASW][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs12895070	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12897227	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17128610	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17128614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17128655	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128657	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17128677	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17128684	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17128690	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17684916	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1951887	0.93[ASW][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1951889	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1951890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2093800	0.94[ASN][1000 genomes]
rs2252189	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274076	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274078	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2274079	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296182	0.93[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap]
rs2296183	0.82[AFR][1000 genomes]
rs2341889	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28458791	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28703642	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34023572	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34111199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34118806	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34184813	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34408323	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34548095	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34697059	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34706911	0.81[ASN][1000 genomes]
rs34709110	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34931260	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35047443	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35094494	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35420484	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35451981	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35531912	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35535838	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35560341	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35790844	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765515	0.81[JPT][hapmap]
rs4457912	1.00[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55760841	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56229542	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60233569	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61381603	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573051	0.91[ASN][1000 genomes]
rs6573053	0.81[JPT][hapmap]
rs6573054	0.81[JPT][hapmap]
rs68127620	0.93[ASN][1000 genomes]
rs7150285	0.93[ASW][hapmap]
rs7154548	0.94[ASN][1000 genomes]
rs7156566	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72719463	0.86[ASN][1000 genomes]
rs8003149	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8006443	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8007183	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8007832	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs8008764	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8011252	0.80[ASN][1000 genomes]
rs8015588	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][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	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1792376	chr14:56108007-56150151	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10483649	NAA30	cis	cerebellum	SCAN
rs10483649	GCH1	cis	cerebellum	SCAN
rs10483649	GCH1	cis	parietal	SCAN
rs10483649	KTN1	cis	parietal	SCAN
rs10483649	KTN1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56078600-56148600	Weak transcription	Stomach Mucosa	stomach
2	chr14:56079800-56111400	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr14:56080800-56110800	Strong transcription	Primary T helper cells PMA-I stimulated	--
4	chr14:56087400-56111800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr14:56087400-56112200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr14:56087400-56132200	Strong transcription	Dnd41	blood
7	chr14:56087600-56110000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:56087600-56145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:56088200-56108600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr14:56088200-56129400	Weak transcription	Spleen	Spleen
11	chr14:56088200-56132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:56088400-56121600	Weak transcription	Aorta	Aorta
13	chr14:56088400-56121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:56088400-56153200	Weak transcription	Gastric	stomach
15	chr14:56092800-56135400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:56093200-56110000	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr14:56093800-56110000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr14:56094200-56110000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr14:56094200-56110200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:56094400-56109800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr14:56094400-56113000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr14:56094400-56132600	Strong transcription	HSMM	muscle
23	chr14:56094600-56110000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:56094600-56110200	Strong transcription	Liver	Liver
25	chr14:56095000-56142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr14:56096200-56112000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr14:56096600-56109400	Strong transcription	GM12878-XiMat	blood
28	chr14:56097600-56115600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:56097600-56145200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:56097600-56155400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:56098600-56121600	Weak transcription	Small Intestine	intestine
32	chr14:56099000-56128000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr14:56099400-56118600	Strong transcription	Hela-S3	cervix
34	chr14:56099800-56110000	Strong transcription	Fetal Thymus	thymus
35	chr14:56100000-56109000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr14:56100200-56131000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr14:56100400-56109800	Strong transcription	Placenta	Placenta
38	chr14:56100400-56110200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr14:56100400-56112600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr14:56100800-56109800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr14:56100800-56109800	Strong transcription	A549	lung
42	chr14:56100800-56112200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr14:56101000-56132800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr14:56101400-56112800	Strong transcription	Primary B cells from cord blood	blood
45	chr14:56101800-56109200	Strong transcription	NHDF-Ad	bronchial
46	chr14:56101800-56118200	Weak transcription	Fetal Brain Female	brain
47	chr14:56101800-56121600	Weak transcription	Pancreas	Pancrea
48	chr14:56101800-56123200	Weak transcription	Fetal Intestine Small	intestine
49	chr14:56101800-56128800	Weak transcription	Fetal Stomach	stomach
50	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain

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