Variant report

Variant	rs11047899
Chromosome Location	chr12:25371904-25371905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:25370682..25374580-chr12:25537849..25540511,3	K562	blood:
2	chr12:25365078..25366619-chr12:25369523..25372416,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10842501	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10842502	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10842504	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10842505	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10842512	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11047887	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11047888	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11047894	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047895	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047896	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047897	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047901	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11047902	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11047905	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1137188	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1137189	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1137196	0.81[AMR][1000 genomes]
rs11608657	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11611468	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12245	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12368504	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12424283	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12578773	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12579073	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12579681	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12579942	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12580030	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12587	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12814233	0.84[AFR][1000 genomes]
rs12815546	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12822857	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13096	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4246228	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4246229	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4494384	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4551857	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4963859	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4963860	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4963861	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5009909	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61762422	0.88[AFR][1000 genomes]
rs6487461	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs712	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7137630	0.92[EUR][1000 genomes]
rs7302922	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7312739	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7955844	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8720	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9266	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv557798	chr12:25359841-25397282	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv898925	chr12:25367669-25398972	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv898926	chr12:25367669-25408047	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11047899	LYRM5	cis	Whole Blood	GTEx
rs11047899	LYRM5	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25348600-25402200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25348600-25403200	Weak transcription	Spleen	Spleen
3	chr12:25349000-25372800	Weak transcription	Aorta	Aorta
4	chr12:25349000-25374200	Weak transcription	Lung	lung
5	chr12:25349000-25386000	Weak transcription	Left Ventricle	heart
6	chr12:25349000-25402400	Weak transcription	Right Ventricle	heart
7	chr12:25349400-25388200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:25349400-25388600	Weak transcription	NHLF	lung
9	chr12:25349400-25393800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:25349400-25396000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:25349400-25401800	Weak transcription	Fetal Brain Male	brain
12	chr12:25349400-25402600	Weak transcription	Brain Germinal Matrix	brain
13	chr12:25349600-25389000	Weak transcription	Brain Angular Gyrus	brain
14	chr12:25349600-25394600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:25349600-25402600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:25349600-25402600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:25349600-25402600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:25349600-25402600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:25349800-25379200	Weak transcription	Brain Anterior Caudate	brain
20	chr12:25349800-25386200	Weak transcription	Hela-S3	cervix
21	chr12:25349800-25390200	Weak transcription	K562	blood
22	chr12:25350000-25372600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:25350000-25402800	Weak transcription	Ovary	ovary
24	chr12:25353200-25378800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:25354000-25402400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:25354400-25378400	Weak transcription	HMEC	breast
27	chr12:25354400-25402200	Weak transcription	Pancreas	Pancrea
28	chr12:25354600-25389000	Weak transcription	HSMMtube	muscle
29	chr12:25355800-25396000	Weak transcription	Small Intestine	intestine
30	chr12:25356200-25372800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:25356600-25377600	Weak transcription	Gastric	stomach
32	chr12:25356600-25402600	Weak transcription	Fetal Heart	heart
33	chr12:25360200-25379200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:25360200-25380200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:25360400-25377000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:25360800-25388600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:25360800-25389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:25360800-25402200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:25361000-25376800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:25361000-25378600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:25361000-25379800	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:25361000-25383800	Weak transcription	NHEK	skin
43	chr12:25361000-25388000	Weak transcription	A549	lung
44	chr12:25361000-25388600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:25361000-25388800	Weak transcription	Esophagus	oesophagus
46	chr12:25361000-25395800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:25361000-25402600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:25361000-25402600	Weak transcription	Fetal Brain Female	brain
49	chr12:25361200-25374200	Weak transcription	Thymus	Thymus
50	chr12:25361200-25388400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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