Variant report

Variant	rs12895366
Chromosome Location	chr14:56159551-56159552
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10136386	0.88[CEU][hapmap]
rs10146870	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10444721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10483644	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10483649	0.80[ASW][hapmap];0.81[JPT][hapmap]
rs10483651	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12432344	0.89[ASN][1000 genomes]
rs12432887	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs12434609	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12434624	0.92[ASN][1000 genomes]
rs12434660	0.91[ASN][1000 genomes]
rs12435643	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12587700	0.95[ASN][1000 genomes]
rs12587705	0.94[ASN][1000 genomes]
rs12587735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588172	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12588185	0.88[ASN][1000 genomes]
rs12589864	0.94[ASN][1000 genomes]
rs12590388	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[ASN][1000 genomes]
rs12590936	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12882850	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12885864	0.95[ASN][1000 genomes]
rs12888809	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12891129	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891526	0.88[EUR][1000 genomes]
rs12893162	0.87[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12897227	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17128614	0.81[JPT][hapmap]
rs17128657	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17128677	0.94[ASN][1000 genomes]
rs17128684	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs17128690	0.95[ASN][1000 genomes]
rs17253737	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17684916	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17684959	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17685650	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951887	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1951889	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2093800	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252189	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2274076	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2274078	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2274079	0.92[ASN][1000 genomes]
rs2296182	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2296183	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28458791	0.94[ASN][1000 genomes]
rs28581272	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28703642	0.93[ASN][1000 genomes]
rs34023572	0.84[ASN][1000 genomes]
rs34111199	0.92[ASN][1000 genomes]
rs34133022	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34408323	0.92[ASN][1000 genomes]
rs34548095	0.95[ASN][1000 genomes]
rs34697059	0.95[ASN][1000 genomes]
rs34706911	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34709110	0.90[ASN][1000 genomes]
rs34853759	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34982220	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35094494	0.94[ASN][1000 genomes]
rs35535838	0.93[ASN][1000 genomes]
rs3765515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs4457912	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55927221	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56229542	0.85[ASN][1000 genomes]
rs60233569	0.95[ASN][1000 genomes]
rs6573051	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6573053	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6573054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68127620	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7150285	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154548	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7156566	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7158176	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719463	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8003149	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs8007183	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007832	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs8008764	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8011252	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8011732	0.80[CEU][hapmap]
rs8015588	0.95[ASN][1000 genomes]
rs942317	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12895366	GCH1	cis	parietal	SCAN
rs12895366	KTN1	cis	multi-tissue	Pritchard
rs12895366	GCH1	cis	cerebellum	SCAN
rs12895366	KTN1	cis	parietal	SCAN
rs12895366	FBXO34	cis	parietal	SCAN
rs12895366	KTN1	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56101800-56162800	Weak transcription	Brain Germinal Matrix	brain
2	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
3	chr14:56109200-56164000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr14:56122400-56164800	Weak transcription	Small Intestine	intestine
5	chr14:56142800-56168400	Weak transcription	Fetal Kidney	kidney
6	chr14:56147400-56170400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr14:56147800-56164200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:56148000-56161800	Weak transcription	Pancreas	Pancrea
9	chr14:56148000-56174000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:56148400-56165600	Weak transcription	NHDF-Ad	bronchial
11	chr14:56151200-56165800	Weak transcription	Hela-S3	cervix
12	chr14:56152200-56162200	Weak transcription	Fetal Intestine Small	intestine
13	chr14:56152800-56164400	Weak transcription	HMEC	breast
14	chr14:56153000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr14:56153200-56160000	Weak transcription	Fetal Heart	heart
16	chr14:56153400-56174000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr14:56153600-56162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr14:56153600-56163200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr14:56153600-56164200	Weak transcription	HSMMtube	muscle
20	chr14:56153600-56164400	Weak transcription	Brain Angular Gyrus	brain
21	chr14:56153600-56165200	Weak transcription	NH-A	brain
22	chr14:56153600-56165600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr14:56153600-56165600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr14:56153600-56165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:56153800-56159600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr14:56153800-56160400	Weak transcription	Gastric	stomach
27	chr14:56153800-56161400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr14:56153800-56162200	Weak transcription	Fetal Intestine Large	intestine
29	chr14:56153800-56163200	Weak transcription	Colonic Mucosa	Colon
30	chr14:56153800-56164000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr14:56153800-56164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:56153800-56164200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:56153800-56165000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr14:56153800-56165600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr14:56153800-56170600	Weak transcription	Fetal Stomach	stomach
36	chr14:56153800-56172000	Weak transcription	Esophagus	oesophagus
37	chr14:56153800-56172400	Weak transcription	Dnd41	blood
38	chr14:56153800-56173800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr14:56153800-56174000	Weak transcription	Brain Anterior Caudate	brain
40	chr14:56154000-56162200	Weak transcription	Ovary	ovary
41	chr14:56154000-56167800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr14:56154000-56172400	Weak transcription	Lung	lung
43	chr14:56154000-56173800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr14:56154000-56177800	Weak transcription	Left Ventricle	heart
45	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
46	chr14:56154200-56162000	Weak transcription	Liver	Liver
47	chr14:56154200-56162200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr14:56154200-56163400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr14:56154400-56163800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr14:56154400-56177800	Weak transcription	Fetal Muscle Leg	muscle

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