Variant report

Variant	rs12432887
Chromosome Location	chr14:56112463-56112464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:56046884..56048461-chr14:56110849..56113567,2	K562	blood:
2	chr14:56110772..56112668-chr14:56115971..56118185,2	K562	blood:

Variant related genes	Relation type
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10136408	0.86[CEU][hapmap]
rs10444721	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10483644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10483649	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]
rs10483651	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12432344	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12432588	0.89[EUR][1000 genomes]
rs12433592	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12434609	0.94[ASN][1000 genomes]
rs12434624	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434660	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12434799	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12435643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12587700	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12587705	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12587735	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs12588172	0.85[ASN][1000 genomes]
rs12588185	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12589864	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12589867	0.91[EUR][1000 genomes]
rs12590388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[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];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12590936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12882850	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12885864	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12888809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12891129	0.92[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];0.92[ASN][1000 genomes]
rs12895070	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12895366	0.92[ASN][1000 genomes]
rs12897227	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs17128610	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17128614	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17128655	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17128657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128677	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[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];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17128690	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17253737	0.92[ASN][1000 genomes]
rs17684916	0.95[ASN][1000 genomes]
rs17684959	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs17685650	0.84[AFR][1000 genomes];0.92[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];0.94[ASN][1000 genomes]
rs1951889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951890	0.94[CEU][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2093800	0.80[ASN][1000 genomes]
rs2252189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2274076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274079	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296182	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2296183	0.92[ASN][1000 genomes]
rs2341889	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28458791	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28581272	0.88[ASN][1000 genomes]
rs28703642	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34023572	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34111199	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34118806	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34133022	0.92[ASN][1000 genomes]
rs34184813	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34408323	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34548095	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34697059	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34706911	0.94[ASN][1000 genomes]
rs34709110	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34853759	0.92[ASN][1000 genomes]
rs34931260	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34982220	0.93[ASN][1000 genomes]
rs35047443	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35094494	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35420484	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35451981	0.91[EUR][1000 genomes]
rs35531912	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35535838	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35560341	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35790844	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3765515	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4457912	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs55760841	0.91[EUR][1000 genomes]
rs55927221	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56229542	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60233569	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61381603	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6573051	0.80[ASN][1000 genomes]
rs6573053	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6573054	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7150285	0.95[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs7154548	0.80[ASN][1000 genomes]
rs7156566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7158176	0.92[ASN][1000 genomes]
rs8003149	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8006443	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8007832	0.82[MEX][hapmap]
rs8015588	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[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
rs12432887	KTN1	cis	cerebellum	SCAN
rs12432887	GCH1	cis	parietal	SCAN
rs12432887	KTN1	cis	parietal	SCAN
rs12432887	NAA30	cis	cerebellum	SCAN
rs12432887	GCH1	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	chr14:56087400-56132200	Strong transcription	Dnd41	blood
3	chr14:56087600-56145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:56088200-56129400	Weak transcription	Spleen	Spleen
5	chr14:56088200-56132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:56088400-56121600	Weak transcription	Aorta	Aorta
7	chr14:56088400-56121800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:56088400-56153200	Weak transcription	Gastric	stomach
9	chr14:56092800-56135400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr14:56094400-56113000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr14:56094400-56132600	Strong transcription	HSMM	muscle
12	chr14:56095000-56142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr14:56097600-56115600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr14:56097600-56145200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:56097600-56155400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:56098600-56121600	Weak transcription	Small Intestine	intestine
17	chr14:56099000-56128000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:56099400-56118600	Strong transcription	Hela-S3	cervix
19	chr14:56100200-56131000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr14:56100400-56112600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr14:56101000-56132800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr14:56101400-56112800	Strong transcription	Primary B cells from cord blood	blood
23	chr14:56101800-56118200	Weak transcription	Fetal Brain Female	brain
24	chr14:56101800-56121600	Weak transcription	Pancreas	Pancrea
25	chr14:56101800-56123200	Weak transcription	Fetal Intestine Small	intestine
26	chr14:56101800-56128800	Weak transcription	Fetal Stomach	stomach
27	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain
28	chr14:56102400-56121600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr14:56102400-56121600	Weak transcription	Esophagus	oesophagus
30	chr14:56102400-56145200	Weak transcription	Lung	lung
31	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
32	chr14:56103200-56117000	Weak transcription	K562	blood
33	chr14:56103400-56130600	Weak transcription	Thymus	Thymus
34	chr14:56104000-56115800	Weak transcription	Brain Angular Gyrus	brain
35	chr14:56104600-56119600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr14:56104600-56121600	Weak transcription	Ovary	ovary
37	chr14:56104600-56127600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr14:56104800-56112600	Weak transcription	HSMMtube	muscle
39	chr14:56104800-56121600	Weak transcription	Left Ventricle	heart
40	chr14:56104800-56128800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:56104800-56157400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr14:56105000-56122600	Weak transcription	NHLF	lung
43	chr14:56105000-56129200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr14:56105000-56138200	Weak transcription	Psoas Muscle	Psoas
45	chr14:56106000-56150200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:56106400-56115000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr14:56107000-56121600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr14:56107600-56115000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr14:56108000-56115000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr14:56108200-56115600	Weak transcription	Brain Cingulate Gyrus	brain

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