Variant report

Variant	rs12909874
Chromosome Location	chr15:52721747-52721748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52721087..52722609-chr15:52853410..52856403,2	MCF-7	breast:
2	chr15:52721403..52723684-chr15:52725842..52728598,2	K562	blood:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1001522	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10083671	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10083673	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1009157	0.80[ASN][1000 genomes]
rs10518687	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1125460	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12898655	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12914979	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1464963	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1464964	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669856	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669858	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669867	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724628	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1724629	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1724631	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1724634	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1724639	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724641	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17542017	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242057	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2242058	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2414150	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2414151	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2444013	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35134548	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35523401	0.98[ASN][1000 genomes]
rs3858907	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4776039	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4776046	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62015999	0.81[ASN][1000 genomes]
rs62023267	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71474804	0.91[ASN][1000 genomes]
rs7176061	1.00[ASN][1000 genomes]
rs7176639	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs722436	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028033	0.81[ASN][1000 genomes]
rs8033626	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8038386	0.80[AMR][1000 genomes]
rs935892	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12909874	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs12909874	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
3	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
7	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
8	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
9	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:52685400-52730000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:52689600-52730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:52689600-52730200	Weak transcription	Left Ventricle	heart
13	chr15:52689600-52730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:52696000-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:52697200-52730000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:52697200-52730400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
18	chr15:52697400-52730400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:52702400-52737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:52702600-52730000	Weak transcription	Brain Anterior Caudate	brain
21	chr15:52702600-52730600	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:52710800-52732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:52711600-52732000	Weak transcription	Brain Germinal Matrix	brain
24	chr15:52713600-52729800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:52714800-52722600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:52715600-52726400	Weak transcription	Psoas Muscle	Psoas
27	chr15:52716600-52722600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:52716600-52732600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:52717200-52730200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:52717800-52722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:52719000-52728000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:52719400-52722600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr15:52719600-52722600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:52719800-52722600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:52719800-52722800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:52720000-52725400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:52720200-52732200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:52720400-52726600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:52720600-52726800	Weak transcription	Fetal Heart	heart
40	chr15:52720600-52729800	Weak transcription	NHEK	skin
41	chr15:52720800-52721800	Weak transcription	HUVEC	blood vessel
42	chr15:52720800-52726600	Weak transcription	Adipose Nuclei	Adipose
43	chr15:52720800-52726800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:52720800-52729200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:52720800-52730400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr15:52720800-52732400	Weak transcription	NHDF-Ad	bronchial
47	chr15:52721000-52722000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:52721000-52722600	Weak transcription	Primary T cells from cord blood	blood
49	chr15:52721000-52722800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr15:52721000-52729200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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