Variant report

Variant	rs12245
Chromosome Location	chr12:25358650-25358651
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25357761..25359956-chr12:25367991..25370766,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10842498	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10842499	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10842501	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842502	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10842504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10842512	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047887	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047888	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11047894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047895	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047897	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047899	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047901	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11047902	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047905	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11047909	0.87[ASN][1000 genomes]
rs1137188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1137189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1137196	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11608657	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611468	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12368504	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12424283	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578773	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579073	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12579681	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12579942	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12580030	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581706	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810577	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12814233	0.92[AFR][1000 genomes]
rs12815546	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12820019	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12822857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17329025	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4246228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4494384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4551857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963860	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4963861	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5009909	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61762422	0.92[AFR][1000 genomes]
rs6487461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137630	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7302922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312739	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7955844	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9266	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898922	chr12:25274593-25408047	Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1048631	chr12:25353517-25378661	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv898923	chr12:25357680-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv898924	chr12:25357680-25398972	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12245	LYRM5	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25360000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
4	chr12:25348800-25359400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:25348800-25360200	Weak transcription	Esophagus	oesophagus
6	chr12:25349000-25360000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:25349000-25360000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:25349000-25360400	Weak transcription	Psoas Muscle	Psoas
9	chr12:25349000-25369200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
11	chr12:25349000-25374200	Weak transcription	Lung	lung
12	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
13	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
14	chr12:25349200-25359000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:25349200-25359400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:25349200-25360800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:25349200-25362400	Weak transcription	Colonic Mucosa	Colon
18	chr12:25349200-25363200	Weak transcription	Brain Substantia Nigra	brain
19	chr12:25349200-25363400	Weak transcription	Stomach Mucosa	stomach
20	chr12:25349400-25359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:25349400-25367400	Weak transcription	Fetal Stomach	stomach
22	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:25349400-25388600	Weak transcription	NHLF	lung
24	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
27	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
28	chr12:25349600-25359200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:25349600-25359200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:25349600-25359400	Weak transcription	Fetal Kidney	kidney
31	chr12:25349600-25359400	Weak transcription	Fetal Lung	lung
32	chr12:25349600-25360000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:25349600-25360000	Weak transcription	Fetal Brain Female	brain
34	chr12:25349600-25360800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:25349600-25364600	Weak transcription	Colon Smooth Muscle	Colon
36	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
37	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr12:25349800-25359800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:25349800-25360000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:25349800-25360000	Weak transcription	Thymus	Thymus
45	chr12:25349800-25360200	Weak transcription	Fetal Muscle Leg	muscle
46	chr12:25349800-25360400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:25349800-25360400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:25349800-25379200	Weak transcription	Brain Anterior Caudate	brain
49	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
50	chr12:25349800-25390200	Weak transcription	K562	blood

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