Variant report

Variant	rs2296182
Chromosome Location	chr14:56136959-56136960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10136386	0.88[CEU][hapmap]
rs10146870	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10444721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483644	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10483649	0.93[ASW][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs10483651	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12432344	0.88[ASN][1000 genomes]
rs12432887	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12434609	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12434624	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12434660	0.90[ASN][1000 genomes]
rs12435643	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12587700	0.95[ASN][1000 genomes]
rs12587705	0.95[ASN][1000 genomes]
rs12587735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588172	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12588185	0.87[ASN][1000 genomes]
rs12589864	0.95[ASN][1000 genomes]
rs12590388	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12590936	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12882850	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12885864	0.95[ASN][1000 genomes]
rs12888809	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12891129	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12891526	0.92[EUR][1000 genomes]
rs12893162	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895366	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12897227	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17128614	0.85[JPT][hapmap]
rs17128655	0.82[AFR][1000 genomes]
rs17128657	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17128677	0.95[ASN][1000 genomes]
rs17128684	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17128690	0.95[ASN][1000 genomes]
rs17253737	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17684916	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17684959	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17685650	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1951889	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1951890	0.92[ASW][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap]
rs2093800	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2252189	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2274076	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2274078	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2274079	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2296183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458791	0.95[ASN][1000 genomes]
rs28581272	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28703642	0.93[ASN][1000 genomes]
rs34023572	0.83[ASN][1000 genomes]
rs34111199	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs34133022	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34408323	0.91[ASN][1000 genomes]
rs34548095	0.95[ASN][1000 genomes]
rs34697059	0.95[ASN][1000 genomes]
rs34706911	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34709110	0.89[ASN][1000 genomes]
rs34853759	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34982220	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35094494	0.93[ASN][1000 genomes]
rs35535838	0.94[ASN][1000 genomes]
rs3765515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4457912	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55927221	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56229542	0.84[ASN][1000 genomes]
rs60233569	0.95[ASN][1000 genomes]
rs6573051	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6573053	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68127620	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7150285	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154548	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7156566	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7158176	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72719463	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8003149	0.93[ASN][1000 genomes]
rs8007183	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8007832	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8008764	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8011252	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8011732	0.84[CEU][hapmap]
rs8015588	0.95[ASN][1000 genomes]
rs942317	0.84[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2296182	KTN1	cis	multi-tissue	Pritchard

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	chr14:56087600-56145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:56088400-56153200	Weak transcription	Gastric	stomach
4	chr14:56095000-56142200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:56097600-56145200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:56097600-56155400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain
8	chr14:56102400-56145200	Weak transcription	Lung	lung
9	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
10	chr14:56104800-56157400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:56105000-56138200	Weak transcription	Psoas Muscle	Psoas
12	chr14:56106000-56150200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr14:56109200-56141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:56109200-56164000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:56109800-56139600	Weak transcription	Colonic Mucosa	Colon
16	chr14:56109800-56145400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr14:56113800-56155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr14:56115000-56155000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr14:56118400-56138400	Weak transcription	HSMMtube	muscle
20	chr14:56119200-56139200	Weak transcription	K562	blood
21	chr14:56120000-56139200	Weak transcription	Brain Angular Gyrus	brain
22	chr14:56122000-56138200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr14:56122000-56145400	Weak transcription	Pancreas	Pancrea
24	chr14:56122200-56138400	Weak transcription	Brain Hippocampus Middle	brain
25	chr14:56122200-56138600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr14:56122400-56145000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:56122400-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:56122400-56152600	Weak transcription	Esophagus	oesophagus
29	chr14:56122400-56164800	Weak transcription	Small Intestine	intestine
30	chr14:56124000-56137400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr14:56124000-56138400	Weak transcription	Brain Substantia Nigra	brain
32	chr14:56124000-56142200	Weak transcription	Fetal Kidney	kidney
33	chr14:56124800-56138200	Weak transcription	Colon Smooth Muscle	Colon
34	chr14:56125000-56144600	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:56125200-56137800	Weak transcription	NHLF	lung
36	chr14:56126200-56137400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr14:56127000-56138200	Weak transcription	HepG2	liver
38	chr14:56128200-56145200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr14:56128200-56149800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr14:56129200-56143800	Weak transcription	Fetal Intestine Small	intestine
41	chr14:56129200-56144600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr14:56129200-56145200	Weak transcription	Fetal Stomach	stomach
43	chr14:56129800-56137200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:56129800-56137600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr14:56129800-56137800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr14:56129800-56137800	Weak transcription	Brain Anterior Caudate	brain
47	chr14:56129800-56137800	Weak transcription	Fetal Brain Female	brain
48	chr14:56129800-56138200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr14:56129800-56138400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr14:56129800-56145000	Weak transcription	Brain Cingulate Gyrus	brain

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