Variant report

Variant	rs17128677
Chromosome Location	chr14:56147696-56147697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10136408	0.86[CEU][hapmap]
rs10444721	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10483644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10483649	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10483651	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12432344	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12432588	0.84[EUR][1000 genomes]
rs12432887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12433592	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12434609	0.91[ASN][1000 genomes]
rs12434624	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12434660	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12434799	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12435643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587700	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587705	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587735	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs12588172	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12588185	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12589864	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12589867	0.86[EUR][1000 genomes]
rs12590388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12590936	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];0.98[ASN][1000 genomes]
rs12882850	0.81[JPT][hapmap]
rs12885864	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12888809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12891129	0.94[ASN][1000 genomes]
rs12891489	0.86[CEU][hapmap]
rs12893162	0.80[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs12895070	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12895366	0.94[ASN][1000 genomes]
rs12897227	0.81[JPT][hapmap]
rs17128610	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17128614	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17128655	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17128657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17128684	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17128690	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17253737	0.94[ASN][1000 genomes]
rs17684916	0.92[ASN][1000 genomes]
rs17684959	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs17685650	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1951887	0.80[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs1951889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1951890	0.94[CEU][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2252189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2274078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274079	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2296182	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2296183	0.95[ASN][1000 genomes]
rs2341889	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28458791	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581272	0.85[ASN][1000 genomes]
rs28703642	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34023572	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34111199	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34118806	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34133022	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34184813	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34408323	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34548095	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34697059	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34706911	0.91[ASN][1000 genomes]
rs34709110	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34853759	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs34931260	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34982220	0.93[ASN][1000 genomes]
rs35047443	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35094494	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35420484	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35451981	0.86[EUR][1000 genomes]
rs35531912	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35535838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35560341	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35790844	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3765515	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4457912	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs55760841	0.86[EUR][1000 genomes]
rs55927221	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56229542	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60233569	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61381603	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6573051	0.80[ASN][1000 genomes]
rs6573053	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573054	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7150285	0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7156566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7158176	0.94[ASN][1000 genomes]
rs8003149	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8006443	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007832	0.82[MEX][hapmap]
rs8015588	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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	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
2	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
3	nsv1283	chr14:56120059-56164729	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17128677	KTN1	cis	cerebellum	SCAN
rs17128677	KTN1	cis	parietal	SCAN
rs17128677	NAA30	cis	cerebellum	SCAN
rs17128677	GCH1	cis	parietal	SCAN
rs17128677	GCH1	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr14:56088400-56153200	Weak transcription	Gastric	stomach
3	chr14:56097600-56155400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain
5	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
6	chr14:56104800-56157400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:56106000-56150200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr14:56109200-56164000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:56113800-56155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:56115000-56155000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr14:56122400-56152600	Weak transcription	Esophagus	oesophagus
12	chr14:56122400-56164800	Weak transcription	Small Intestine	intestine
13	chr14:56128200-56149800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:56129800-56152000	Weak transcription	Aorta	Aorta
15	chr14:56133400-56153400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr14:56134000-56155000	Strong transcription	HSMM	muscle
17	chr14:56134200-56153600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr14:56134600-56154200	Strong transcription	Liver	Liver
19	chr14:56134800-56148200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr14:56135000-56153400	Strong transcription	Placenta	Placenta
21	chr14:56135200-56152800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr14:56135200-56153600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr14:56136600-56154200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr14:56136800-56150000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:56136800-56153800	Strong transcription	Dnd41	blood
26	chr14:56136800-56154200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr14:56137000-56153600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr14:56137000-56153800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr14:56137000-56154200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr14:56137200-56153600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr14:56137200-56154000	Strong transcription	Primary B cells from cord blood	blood
32	chr14:56137400-56149400	Strong transcription	HMEC	breast
33	chr14:56137400-56153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr14:56137400-56154800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr14:56137400-56154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr14:56137400-56155000	Strong transcription	Adipose Nuclei	Adipose
37	chr14:56138200-56148200	Strong transcription	Colon Smooth Muscle	Colon
38	chr14:56138600-56151600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr14:56138600-56155200	Strong transcription	A549	lung
40	chr14:56138800-56153600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr14:56141400-56154400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr14:56141600-56149600	Strong transcription	GM12878-XiMat	blood
43	chr14:56142800-56168400	Weak transcription	Fetal Kidney	kidney
44	chr14:56143600-56149600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr14:56143600-56149800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr14:56144200-56148000	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr14:56144200-56150800	Strong transcription	Fetal Thymus	thymus
48	chr14:56144400-56147800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr14:56144600-56148400	Strong transcription	Fetal Muscle Leg	muscle
50	chr14:56144600-56148600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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