Variant report

Variant	rs12588172
Chromosome Location	chr14:56159354-56159355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10136386	0.88[CEU][hapmap]
rs10146870	1.00[CEU][hapmap]
rs10444721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10483644	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10483649	0.81[JPT][hapmap]
rs10483651	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12432344	0.82[ASN][1000 genomes]
rs12432887	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs12434609	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12434624	0.85[ASN][1000 genomes]
rs12434660	0.84[ASN][1000 genomes]
rs12435643	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12587700	0.88[ASN][1000 genomes]
rs12587705	0.87[ASN][1000 genomes]
rs12587735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12588185	0.95[ASN][1000 genomes]
rs12589864	0.87[ASN][1000 genomes]
rs12590388	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.85[ASN][1000 genomes]
rs12590936	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12882850	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12885864	0.88[ASN][1000 genomes]
rs12888809	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12891129	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12891526	0.85[EUR][1000 genomes]
rs12893162	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12895366	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12897227	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17128614	0.81[JPT][hapmap]
rs17128657	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17128677	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs17128684	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17128690	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17253737	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17684916	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17684959	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17685650	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1951887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1951889	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2093800	0.87[EUR][1000 genomes]
rs2252189	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2274076	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2274078	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2274079	0.85[ASN][1000 genomes]
rs2296182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap]
rs2296183	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28458791	0.87[ASN][1000 genomes]
rs28581272	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28703642	0.85[ASN][1000 genomes]
rs34023572	0.82[ASN][1000 genomes]
rs34111199	0.84[ASN][1000 genomes]
rs34133022	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34408323	0.84[ASN][1000 genomes]
rs34548095	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34697059	0.88[ASN][1000 genomes]
rs34706911	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34709110	0.82[ASN][1000 genomes]
rs34853759	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34982220	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35094494	0.87[ASN][1000 genomes]
rs35535838	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3765515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4457912	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs55927221	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60233569	0.95[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6573051	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6573053	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6573054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs68127620	0.80[EUR][1000 genomes]
rs7150285	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7154548	0.87[EUR][1000 genomes]
rs7156566	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs7158176	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72719463	0.84[EUR][1000 genomes]
rs8003149	0.87[ASN][1000 genomes]
rs8007183	0.85[EUR][1000 genomes]
rs8007832	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs8008764	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8011732	0.80[CEU][hapmap]
rs8015588	0.82[AFR][1000 genomes];0.88[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
rs12588172	GCH1	cis	parietal	SCAN
rs12588172	KTN1	cis	cerebellum	SCAN
rs12588172	GCH1	cis	cerebellum	SCAN
rs12588172	FBXO34	cis	parietal	SCAN
rs12588172	KTN1	cis	parietal	SCAN
rs12588172	KTN1	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 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	chr14:56152400-56159400	Weak transcription	Colon Smooth Muscle	Colon
14	chr14:56152800-56164400	Weak transcription	HMEC	breast
15	chr14:56153000-56167800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr14:56153200-56160000	Weak transcription	Fetal Heart	heart
17	chr14:56153400-56174000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr14:56153600-56162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:56153600-56163200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr14:56153600-56164200	Weak transcription	HSMMtube	muscle
21	chr14:56153600-56164400	Weak transcription	Brain Angular Gyrus	brain
22	chr14:56153600-56165200	Weak transcription	NH-A	brain
23	chr14:56153600-56165600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr14:56153600-56165600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr14:56153600-56165800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:56153800-56159400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr14:56153800-56159600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:56153800-56160400	Weak transcription	Gastric	stomach
29	chr14:56153800-56161400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr14:56153800-56162200	Weak transcription	Fetal Intestine Large	intestine
31	chr14:56153800-56163200	Weak transcription	Colonic Mucosa	Colon
32	chr14:56153800-56164000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:56153800-56164000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:56153800-56164200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr14:56153800-56165000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:56153800-56165600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr14:56153800-56170600	Weak transcription	Fetal Stomach	stomach
38	chr14:56153800-56172000	Weak transcription	Esophagus	oesophagus
39	chr14:56153800-56172400	Weak transcription	Dnd41	blood
40	chr14:56153800-56173800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr14:56153800-56174000	Weak transcription	Brain Anterior Caudate	brain
42	chr14:56154000-56162200	Weak transcription	Ovary	ovary
43	chr14:56154000-56167800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr14:56154000-56172400	Weak transcription	Lung	lung
45	chr14:56154000-56173800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr14:56154000-56177800	Weak transcription	Left Ventricle	heart
47	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
48	chr14:56154200-56162000	Weak transcription	Liver	Liver
49	chr14:56154200-56162200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr14:56154200-56163400	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links