Variant report

Variant	rs1196854
Chromosome Location	chr12:105578110-105578111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1109432	0.92[EUR][1000 genomes]
rs11112414	0.84[ASN][1000 genomes]
rs11610656	0.81[ASN][1000 genomes]
rs1196750	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1196752	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1196758	0.81[EUR][1000 genomes]
rs1196766	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196767	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1196768	0.93[EUR][1000 genomes]
rs1196776	0.93[EUR][1000 genomes]
rs1196778	0.93[EUR][1000 genomes]
rs1196779	0.90[EUR][1000 genomes]
rs1196781	0.90[EUR][1000 genomes]
rs1196785	0.86[EUR][1000 genomes]
rs1196788	0.88[EUR][1000 genomes]
rs1196803	0.96[ASN][1000 genomes]
rs1196804	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196809	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196810	0.94[ASN][1000 genomes]
rs1196812	0.94[ASN][1000 genomes]
rs1196814	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1196816	0.94[ASN][1000 genomes]
rs1196821	0.91[ASN][1000 genomes]
rs1196822	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196826	0.93[ASN][1000 genomes]
rs1196827	0.93[ASN][1000 genomes]
rs1196828	0.93[ASN][1000 genomes]
rs1196829	0.93[ASN][1000 genomes]
rs1196835	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1196836	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1196837	0.92[ASN][1000 genomes]
rs1196838	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1196840	0.92[ASN][1000 genomes]
rs1196843	0.89[ASN][1000 genomes]
rs1196846	0.92[ASN][1000 genomes]
rs1196850	0.91[ASN][1000 genomes]
rs1196855	0.97[ASN][1000 genomes]
rs1196856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196858	0.99[ASN][1000 genomes]
rs1196860	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196865	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1196866	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196867	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196868	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1196870	0.96[ASN][1000 genomes]
rs1196876	0.96[ASN][1000 genomes]
rs1196877	0.96[ASN][1000 genomes]
rs1196878	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196880	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1201657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1201658	0.92[ASN][1000 genomes]
rs1732371	0.89[ASN][1000 genomes]
rs1732377	0.80[EUR][1000 genomes]
rs1732378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1732379	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1732384	0.95[ASN][1000 genomes]
rs2246510	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2264066	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374448	0.86[EUR][1000 genomes]
rs2440693	0.80[EUR][1000 genomes]
rs2440708	0.93[EUR][1000 genomes]
rs2440713	0.96[ASN][1000 genomes]
rs2440717	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2440719	0.94[ASN][1000 genomes]
rs4964127	0.85[EUR][1000 genomes]
rs4964346	0.84[EUR][1000 genomes]
rs6539196	0.84[EUR][1000 genomes]
rs727888	0.93[EUR][1000 genomes]
rs7309320	0.85[EUR][1000 genomes]
rs7310488	0.86[EUR][1000 genomes]
rs7969800	0.84[EUR][1000 genomes]
rs9143	0.98[ASN][1000 genomes]

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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv870352	chr12:105557770-105589263	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1196854	APPL2	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
2	chr12:105524600-105578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
4	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:105556200-105583400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:105558200-105578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:105558200-105578400	Weak transcription	Right Ventricle	heart
8	chr12:105558200-105587200	Weak transcription	Psoas Muscle	Psoas
9	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:105559400-105578800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:105560800-105581800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:105564000-105582200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:105568000-105589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:105568200-105578200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:105568200-105578400	Weak transcription	Esophagus	oesophagus
17	chr12:105568200-105581800	Weak transcription	Small Intestine	intestine
18	chr12:105568400-105578200	Weak transcription	Pancreas	Pancrea
19	chr12:105568400-105581000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:105568600-105578800	Weak transcription	HepG2	liver
21	chr12:105569000-105578200	Weak transcription	Aorta	Aorta
22	chr12:105569600-105578200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:105569600-105578400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:105569600-105578400	Weak transcription	Spleen	Spleen
25	chr12:105569600-105581000	Weak transcription	Hela-S3	cervix
26	chr12:105569800-105578200	Weak transcription	Dnd41	blood
27	chr12:105570000-105579000	Weak transcription	NHEK	skin
28	chr12:105570200-105579000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:105570400-105578400	Weak transcription	Colonic Mucosa	Colon
30	chr12:105570800-105579200	Weak transcription	HSMMtube	muscle
31	chr12:105571000-105578200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr12:105571000-105578200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:105571000-105581800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:105571200-105578200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:105571200-105579000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:105571400-105578400	Weak transcription	HMEC	breast
37	chr12:105571400-105617800	Weak transcription	K562	blood
38	chr12:105572400-105578200	Weak transcription	Fetal Stomach	stomach
39	chr12:105572400-105579000	Weak transcription	NH-A	brain
40	chr12:105572600-105578400	Weak transcription	NHLF	lung
41	chr12:105572600-105579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:105573000-105578400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:105573200-105578200	Weak transcription	A549	lung
44	chr12:105573200-105579000	Weak transcription	GM12878-XiMat	blood
45	chr12:105573200-105579000	Weak transcription	HSMM	muscle
46	chr12:105576000-105580200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:105576000-105593200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:105576200-105578200	Weak transcription	Fetal Intestine Small	intestine
50	chr12:105576400-105578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links