Variant report

Variant	rs55742982
Chromosome Location	chr2:191113359-191113360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 203 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:201)

rs_ID	r²[population]
rs10173593	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10183133	0.85[EUR][1000 genomes]
rs10188044	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10191068	0.85[EUR][1000 genomes]
rs10196013	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10196351	0.87[EUR][1000 genomes]
rs10200496	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10209516	0.84[EUR][1000 genomes]
rs10209984	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1058180	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1058227	0.83[EUR][1000 genomes]
rs1058230	0.83[EUR][1000 genomes]
rs10931448	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1114863	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11216	0.85[EUR][1000 genomes]
rs11542	0.83[EUR][1000 genomes]
rs11683636	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11683763	0.86[EUR][1000 genomes]
rs11684995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685119	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11689196	0.82[EUR][1000 genomes]
rs11689666	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11692448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11695166	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11883568	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11888626	0.88[EUR][1000 genomes]
rs11894667	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11894766	0.85[EUR][1000 genomes]
rs13010589	0.85[EUR][1000 genomes]
rs13011138	0.87[EUR][1000 genomes]
rs13405019	0.86[EUR][1000 genomes]
rs13415995	0.85[EUR][1000 genomes]
rs13416673	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1366672	0.87[EUR][1000 genomes]
rs1583878	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16832420	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16832456	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16832512	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs176712	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1866849	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1866850	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1972288	0.85[EUR][1000 genomes]
rs2099127	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2099128	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2099129	0.88[EUR][1000 genomes]
rs2136567	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2136570	0.83[AMR][1000 genomes]
rs2136571	0.83[AMR][1000 genomes]
rs2244075	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2244076	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2256301	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2271270	0.85[EUR][1000 genomes]
rs2303827	0.88[EUR][1000 genomes]
rs2353890	0.85[EUR][1000 genomes]
rs2354871	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2562796	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2582738	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2582739	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2582740	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2582742	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2582743	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2582744	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2582745	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2582747	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2582749	0.80[AMR][1000 genomes]
rs2582757	0.87[EUR][1000 genomes]
rs2582762	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2582763	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2582769	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2582771	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2582772	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2582773	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2664241	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2664242	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2664243	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664244	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2664246	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664247	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2664249	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2664255	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2664256	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2664261	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2664264	0.86[EUR][1000 genomes]
rs2664266	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664267	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2664269	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2664272	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2664273	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2664274	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2664275	0.88[EUR][1000 genomes]
rs2664276	0.86[EUR][1000 genomes]
rs2664277	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28887221	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291402	0.88[EUR][1000 genomes]
rs291403	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291404	0.88[EUR][1000 genomes]
rs291405	0.88[EUR][1000 genomes]
rs291407	0.88[EUR][1000 genomes]
rs291409	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291410	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291411	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291412	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291413	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291414	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291415	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs291418	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291419	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291420	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291421	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs291422	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs291423	0.87[EUR][1000 genomes]
rs291424	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291425	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291426	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs291434	0.80[AMR][1000 genomes]
rs291435	0.80[AMR][1000 genomes]
rs291436	0.83[AMR][1000 genomes]
rs291439	0.80[AMR][1000 genomes]
rs291440	0.83[AMR][1000 genomes]
rs291441	0.83[AMR][1000 genomes]
rs291442	0.83[AMR][1000 genomes]
rs291450	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs291451	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs291455	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs291456	0.83[AMR][1000 genomes]
rs2919675	0.86[AMR][1000 genomes]
rs2919676	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2941092	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2966470	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34760043	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35214387	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3749015	0.83[EUR][1000 genomes]
rs3749016	0.83[EUR][1000 genomes]
rs3762548	0.85[EUR][1000 genomes]
rs3791788	0.85[EUR][1000 genomes]
rs3791789	0.85[EUR][1000 genomes]
rs3791790	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3791791	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3791792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791800	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3791805	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791806	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3815961	0.85[EUR][1000 genomes]
rs3828269	0.85[EUR][1000 genomes]
rs4146044	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4853503	0.88[EUR][1000 genomes]
rs4853684	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4853685	0.83[EUR][1000 genomes]
rs4853687	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4853688	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4853689	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4853693	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55684836	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55815425	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56742312	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56853355	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57110838	0.84[EUR][1000 genomes]
rs57199157	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58400804	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60068799	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60469543	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61038868	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434381	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434382	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6434383	0.80[EUR][1000 genomes]
rs66738092	0.85[EUR][1000 genomes]
rs66867328	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6720060	0.87[EUR][1000 genomes]
rs6723792	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6737514	0.88[EUR][1000 genomes]
rs6737846	0.85[EUR][1000 genomes]
rs6749512	0.87[EUR][1000 genomes]
rs6751238	0.85[EUR][1000 genomes]
rs6751588	0.85[EUR][1000 genomes]
rs6752703	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6753459	0.85[EUR][1000 genomes]
rs67791002	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs713425	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs713426	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72625301	0.85[EUR][1000 genomes]
rs72625302	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72627903	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72627904	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72627905	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7371399	0.81[EUR][1000 genomes]
rs7371409	0.83[EUR][1000 genomes]
rs7562807	0.85[EUR][1000 genomes]
rs7565423	0.85[EUR][1000 genomes]
rs7566380	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7567973	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7569296	0.85[EUR][1000 genomes]
rs7573689	0.88[EUR][1000 genomes]
rs7574028	0.88[EUR][1000 genomes]
rs7574495	0.85[EUR][1000 genomes]
rs7580863	0.88[EUR][1000 genomes]
rs7582209	0.88[EUR][1000 genomes]
rs7583250	0.85[EUR][1000 genomes]
rs7590942	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7599085	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7602400	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs760307	0.81[EUR][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	esv3439178	chr2:190877215-191124499	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	nsv875620	chr2:191100723-191141593	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55742982	INPP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191056800-191124600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:191056800-191131800	Weak transcription	NHEK	skin
3	chr2:191060800-191180000	Weak transcription	Small Intestine	intestine
4	chr2:191089000-191128800	Weak transcription	Gastric	stomach
5	chr2:191096800-191117400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:191098400-191114800	Weak transcription	HUVEC	blood vessel
7	chr2:191099400-191131800	Weak transcription	HMEC	breast
8	chr2:191100000-191122400	Weak transcription	Colonic Mucosa	Colon
9	chr2:191100000-191150400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:191100400-191128000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:191104400-191151000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:191105000-191180000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:191105800-191115200	Weak transcription	Psoas Muscle	Psoas
14	chr2:191106000-191117200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:191106200-191117200	Strong transcription	Liver	Liver
16	chr2:191106200-191117400	Strong transcription	Adipose Nuclei	Adipose
17	chr2:191106200-191132200	Weak transcription	Hela-S3	cervix
18	chr2:191106600-191117200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:191106600-191131800	Weak transcription	NHLF	lung
20	chr2:191106800-191113800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:191106800-191117200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:191106800-191118000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:191107000-191122400	Strong transcription	Primary B cells from cord blood	blood
24	chr2:191107400-191122800	Weak transcription	HSMMtube	muscle
25	chr2:191107400-191150600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:191107600-191117200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:191107800-191125600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:191108000-191116000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:191108000-191117000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:191108000-191129400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:191108200-191122400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:191108200-191129200	Weak transcription	Spleen	Spleen
33	chr2:191108200-191135400	Weak transcription	Right Ventricle	heart
34	chr2:191108200-191180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:191108800-191118200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:191108800-191124600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:191109000-191122400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:191109200-191115200	Weak transcription	Fetal Heart	heart
39	chr2:191109200-191117000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:191109200-191119800	Weak transcription	Left Ventricle	heart
41	chr2:191109600-191113600	Weak transcription	Fetal Stomach	stomach
42	chr2:191109600-191114800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:191109600-191114800	Weak transcription	Fetal Kidney	kidney
44	chr2:191109600-191115000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:191109600-191115000	Weak transcription	Brain Substantia Nigra	brain
46	chr2:191109600-191116000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:191109600-191116000	Weak transcription	Pancreas	Pancrea
48	chr2:191109600-191116600	Weak transcription	Brain Angular Gyrus	brain
49	chr2:191109600-191116800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:191109600-191120000	Weak transcription	Colon Smooth Muscle	Colon

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