Variant report

Variant	rs12438469
Chromosome Location	chr15:52185448-52185449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1025185	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10519323	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10519325	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442283	1.00[EUR][1000 genomes]
rs1378891	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1426085	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1426086	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649047	1.00[EUR][1000 genomes]
rs17649178	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17649255	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649391	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649692	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17649801	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17649826	1.00[AFR][1000 genomes]
rs17705530	1.00[EUR][1000 genomes]
rs17705649	1.00[EUR][1000 genomes]
rs17705685	1.00[EUR][1000 genomes]
rs17705889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17706076	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2052707	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2162224	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263946	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2436664	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470609	0.97[ASN][1000 genomes]
rs2470613	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554309	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554310	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554311	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554317	0.83[ASN][1000 genomes]
rs2554318	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2554321	0.83[ASN][1000 genomes]
rs2554323	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554325	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554326	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554330	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2554333	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554341	0.85[ASN][1000 genomes]
rs2554351	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554352	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554356	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570219	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570220	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570221	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570225	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2570227	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570234	0.97[ASN][1000 genomes]
rs2570242	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570244	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570245	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570246	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2570247	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570249	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570250	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2570256	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570257	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570259	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570261	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570262	0.90[ASN][1000 genomes]
rs2570267	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570270	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570273	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2570274	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2593165	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593175	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593176	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593180	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623246	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623248	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2623250	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623252	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623253	0.97[ASN][1000 genomes]
rs2623257	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623260	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623261	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2623264	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623267	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623268	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623269	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623277	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623278	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623287	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623293	0.83[ASN][1000 genomes]
rs2899483	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2916174	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959297	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099570	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34407523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794533	1.00[EUR][1000 genomes]
rs3794537	1.00[EUR][1000 genomes]
rs4774600	1.00[EUR][1000 genomes]
rs4774601	1.00[EUR][1000 genomes]
rs4775979	1.00[EUR][1000 genomes]
rs4775987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775988	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775989	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166322	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170700	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173661	1.00[EUR][1000 genomes]
rs7179139	1.00[EUR][1000 genomes]
rs73411105	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74013606	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8024441	1.00[EUR][1000 genomes]
rs8026507	1.00[EUR][1000 genomes]
rs8027426	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8042310	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919056	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs919057	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990666	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52155600-52192000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:52156000-52211000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52163000-52186800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:52163400-52186200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:52167200-52186200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:52167200-52210800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:52167600-52192000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:52167600-52199600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:52167800-52188600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:52168600-52188600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:52170400-52186400	Weak transcription	Thymus	Thymus
12	chr15:52170400-52186600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:52170600-52186000	Weak transcription	Left Ventricle	heart
14	chr15:52171000-52210800	Weak transcription	Right Ventricle	heart
15	chr15:52171200-52190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:52171600-52187000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:52172200-52186000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:52172200-52186600	Weak transcription	Fetal Kidney	kidney
19	chr15:52172200-52190200	Weak transcription	Fetal Heart	heart
20	chr15:52172200-52192000	Weak transcription	Fetal Brain Male	brain
21	chr15:52172800-52208200	Weak transcription	Brain Angular Gyrus	brain
22	chr15:52176400-52188600	Weak transcription	Small Intestine	intestine
23	chr15:52176600-52189000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:52177000-52188200	Weak transcription	Aorta	Aorta
25	chr15:52177000-52189800	Weak transcription	Colonic Mucosa	Colon
26	chr15:52177000-52192400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:52177000-52192400	Weak transcription	Gastric	stomach
28	chr15:52177000-52192400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:52177200-52188600	Weak transcription	Brain Anterior Caudate	brain
30	chr15:52177200-52192400	Weak transcription	Psoas Muscle	Psoas
31	chr15:52177200-52213600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:52177400-52186000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:52177400-52186200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:52177400-52187600	Weak transcription	Ovary	ovary
35	chr15:52177400-52188600	Weak transcription	HSMMtube	muscle
36	chr15:52177400-52188600	Weak transcription	NHLF	lung
37	chr15:52177400-52190000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:52177600-52186000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:52178600-52192400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr15:52178800-52192400	Weak transcription	Spleen	Spleen
41	chr15:52178800-52216600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:52179000-52192400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:52179000-52196400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:52179000-52196600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:52179000-52196600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:52179600-52203800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:52179800-52196000	Strong transcription	HSMM	muscle
49	chr15:52179800-52197200	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:52179800-52197400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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