Variant report

Variant	rs12487499
Chromosome Location	chr3:119349542-119349543
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119297851..119299731-chr3:119347893..119350770,2	MCF-7	breast:
2	chr3:119348305..119350713-chr3:119351647..119354186,2	MCF-7	breast:
3	chr3:119298163..119299885-chr3:119348210..119351201,3	MCF-7	breast:
4	chr3:119349377..119351910-chr3:119353160..119355843,2	K562	blood:

Variant related genes	Relation type
ENSG00000144843	Chromatin interaction
ENSG00000242052	Chromatin interaction
ENSG00000272967	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11914676	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11923223	0.87[ASN][1000 genomes]
rs12488460	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490779	0.99[ASN][1000 genomes]
rs12492456	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403631	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525836	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830115	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830291	0.87[ASN][1000 genomes]
rs17203235	0.99[ASN][1000 genomes]
rs1797827	0.92[ASN][1000 genomes]
rs1872432	0.87[ASN][1000 genomes]
rs1985121	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280578	0.87[ASN][1000 genomes]
rs2670292	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688629	0.92[ASN][1000 genomes]
rs2688630	0.92[ASN][1000 genomes]
rs2688631	0.92[ASN][1000 genomes]
rs2688634	0.97[ASN][1000 genomes]
rs2692616	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2698283	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34097211	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34593263	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34787881	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35043554	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35256565	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4234662	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4629367	0.87[ASN][1000 genomes]
rs4687869	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688021	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688024	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524043	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs525916	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540420	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs572119	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs575833	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs579196	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67683909	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6783324	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6789941	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6790938	0.91[ASN][1000 genomes]
rs6792417	0.87[ASN][1000 genomes]
rs6803814	0.87[ASN][1000 genomes]
rs68150601	0.86[ASN][1000 genomes]
rs71325388	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71325389	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7613825	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8422	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9876919	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv1795621	chr3:119344693-119353995	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1795670	chr3:119347400-119353995	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv1797032	chr3:119347400-119353995	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv1800265	chr3:119347400-119353995	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv591364	chr3:119348130-119353995	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12487499	RP11-190C22.1	cis	Heart Left Ventricle	GTEx
rs12487499	COX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119340800-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:119341400-119364600	Weak transcription	Liver	Liver
3	chr3:119343800-119351400	Enhancers	Psoas Muscle	Psoas
4	chr3:119344200-119349600	Enhancers	Spleen	Spleen
5	chr3:119344400-119351000	Weak transcription	Pancreas	Pancrea
6	chr3:119344600-119352000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:119344800-119350000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:119345000-119349800	Enhancers	Right Ventricle	heart
9	chr3:119345000-119350000	Enhancers	Adipose Nuclei	Adipose
10	chr3:119345200-119350800	Weak transcription	Fetal Heart	heart
11	chr3:119345200-119357600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:119345800-119355200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:119346000-119351400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:119346200-119349800	Enhancers	Right Atrium	heart
15	chr3:119346200-119351000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:119346400-119350800	Enhancers	Placenta	Placenta
17	chr3:119346400-119351200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:119346600-119350400	Enhancers	HSMMtube	muscle
19	chr3:119346800-119350600	Enhancers	Osteobl	bone
20	chr3:119346800-119352600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:119347600-119350400	Enhancers	HSMM	muscle
22	chr3:119347800-119350000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:119347800-119356400	Weak transcription	Fetal Thymus	thymus
24	chr3:119348200-119350000	Enhancers	GM12878-XiMat	blood
25	chr3:119348400-119349800	Weak transcription	Aorta	Aorta
26	chr3:119348800-119349800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:119348800-119349800	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:119348800-119349800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:119348800-119349800	Enhancers	Left Ventricle	heart
30	chr3:119348800-119350000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:119348800-119350200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:119349000-119349800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:119349000-119349800	Enhancers	Colon Smooth Muscle	Colon
34	chr3:119349000-119349800	Enhancers	Ovary	ovary
35	chr3:119349000-119350000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr3:119349000-119350000	Enhancers	HUVEC	blood vessel
37	chr3:119349000-119350000	Enhancers	NHDF-Ad	bronchial
38	chr3:119349000-119350000	Enhancers	NHLF	lung
39	chr3:119349000-119350200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:119349000-119350600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr3:119349000-119351200	Enhancers	Rectal Smooth Muscle	rectum
42	chr3:119349000-119351400	Enhancers	K562	blood
43	chr3:119349200-119349600	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:119349200-119349600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:119349200-119349600	Enhancers	Fetal Stomach	stomach
46	chr3:119349200-119349800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:119349200-119349800	Enhancers	Fetal Muscle Leg	muscle
48	chr3:119349200-119349800	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:119349200-119350000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr3:119349200-119350000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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