Variant report

Variant	rs12961307
Chromosome Location	chr18:12513416-12513417
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	chr18:12511013..12513925-chr18:12546965..12549952,2	K562	blood:
2	chr18:12512543..12514903-chr18:12518908..12520482,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1105748	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs11664013	1.00[CHD][hapmap]
rs12954350	1.00[ASN][1000 genomes]
rs12954606	1.00[ASN][1000 genomes]
rs12955162	1.00[ASN][1000 genomes]
rs12956026	1.00[ASN][1000 genomes]
rs12956686	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957011	1.00[ASN][1000 genomes]
rs12957283	1.00[ASN][1000 genomes]
rs12958301	1.00[ASN][1000 genomes]
rs12959199	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap];1.00[ASN][1000 genomes]
rs12959459	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12961711	1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12964717	1.00[ASN][1000 genomes]
rs12967250	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12970939	1.00[ASN][1000 genomes]
rs12971000	1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17524639	1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs17525459	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs17525599	1.00[ASW][hapmap];1.00[CHD][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs17615525	1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17615801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615991	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs34054541	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34084006	1.00[ASN][1000 genomes]
rs34088731	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34180475	1.00[ASN][1000 genomes]
rs34183067	1.00[ASN][1000 genomes]
rs34215298	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	1.00[ASN][1000 genomes]
rs34371240	1.00[ASN][1000 genomes]
rs34448712	0.83[AFR][1000 genomes]
rs34460164	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34469203	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34512782	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34737110	1.00[ASN][1000 genomes]
rs34859829	1.00[ASN][1000 genomes]
rs34923819	1.00[ASN][1000 genomes]
rs34933611	1.00[ASN][1000 genomes]
rs35082337	1.00[ASN][1000 genomes]
rs35160505	1.00[ASN][1000 genomes]
rs35190325	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35280383	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35309605	1.00[ASN][1000 genomes]
rs35532404	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	1.00[ASN][1000 genomes]
rs35616981	1.00[ASN][1000 genomes]
rs35744165	1.00[ASN][1000 genomes]
rs35815040	1.00[ASN][1000 genomes]
rs35826479	1.00[ASN][1000 genomes]
rs35864675	1.00[ASN][1000 genomes]
rs35939870	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4510091	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45541436	1.00[ASN][1000 genomes]
rs71351482	1.00[ASN][1000 genomes]
rs71351484	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351485	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs71351491	1.00[ASN][1000 genomes]
rs71351492	1.00[ASN][1000 genomes]
rs71351494	1.00[ASN][1000 genomes]
rs71351495	1.00[ASN][1000 genomes]
rs71351501	1.00[ASN][1000 genomes]
rs71353221	1.00[ASN][1000 genomes]
rs71353222	1.00[ASN][1000 genomes]
rs71363149	1.00[ASN][1000 genomes]
rs919	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.91[AFR][1000 genomes];1.00[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers 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	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv2208	chr18:12472999-12518189	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	esv2756075	chr18:12481377-12548970	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12961307	RP11-861E21.1	cis	Artery Tibial	GTEx
rs12961307	SLMO1	cis	Artery Aorta	GTEx
rs12961307	SLMO1	cis	Nerve Tibial	GTEx
rs12961307	SLMO1	cis	Thyroid	GTEx
rs12961307	SLMO1	cis	Esophagus Mucosa	GTEx
rs12961307	RP11-861E21.2	cis	Thyroid	GTEx
rs12961307	SLMO1	cis	Adipose Subcutaneous	GTEx
rs12961307	SLMO1	cis	Artery Tibial	GTEx
rs12961307	AP001029.1	cis	Esophagus Muscularis	GTEx
rs12961307	SLMO1	cis	lung	GTEx
rs12961307	AP001029.1	cis	Thyroid	GTEx
rs12961307	SPIRE1	cis	multi-tissue	Pritchard
rs12961307	AP001029.1	cis	Artery Aorta	GTEx
rs12961307	SLMO1	cis	Esophagus Muscularis	GTEx
rs12961307	AP001029.1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12460200-12516600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12478800-12514200	Weak transcription	NH-A	brain
3	chr18:12478800-12515800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr18:12478800-12515800	Weak transcription	Placenta	Placenta
5	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
6	chr18:12492200-12530400	Weak transcription	HepG2	liver
7	chr18:12492200-12532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr18:12492200-12548600	Weak transcription	Fetal Kidney	kidney
9	chr18:12492400-12515600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr18:12493000-12541200	Weak transcription	NHEK	skin
11	chr18:12493200-12518400	Weak transcription	Esophagus	oesophagus
12	chr18:12493200-12520000	Weak transcription	Colon Smooth Muscle	Colon
13	chr18:12493200-12520400	Weak transcription	Psoas Muscle	Psoas
14	chr18:12493200-12551800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr18:12493400-12515800	Weak transcription	Brain Substantia Nigra	brain
16	chr18:12494000-12515000	Weak transcription	Fetal Lung	lung
17	chr18:12494200-12515000	Weak transcription	HUVEC	blood vessel
18	chr18:12494400-12515600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr18:12495400-12515800	Weak transcription	NHDF-Ad	bronchial
20	chr18:12496000-12515000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr18:12497600-12518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:12500800-12520600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr18:12502000-12520600	Weak transcription	Fetal Stomach	stomach
24	chr18:12505200-12515800	Weak transcription	Brain Hippocampus Middle	brain
25	chr18:12505200-12516200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:12505200-12536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:12505400-12516000	Weak transcription	Brain Angular Gyrus	brain
28	chr18:12505400-12529400	Weak transcription	HMEC	breast
29	chr18:12505600-12520000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:12506400-12515600	Weak transcription	Brain Germinal Matrix	brain
31	chr18:12506400-12516000	Weak transcription	Fetal Heart	heart
32	chr18:12506600-12515600	Weak transcription	Brain Anterior Caudate	brain
33	chr18:12506600-12515600	Weak transcription	Left Ventricle	heart
34	chr18:12506600-12516200	Weak transcription	Right Ventricle	heart
35	chr18:12506800-12515600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr18:12506800-12516000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:12507000-12513800	Weak transcription	Fetal Brain Female	brain
38	chr18:12507000-12514000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr18:12507000-12515600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr18:12507000-12516200	Weak transcription	Aorta	Aorta
41	chr18:12507000-12516400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr18:12507000-12526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr18:12507200-12515600	Weak transcription	Osteobl	bone
44	chr18:12507400-12515400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr18:12507400-12515600	Weak transcription	K562	blood
46	chr18:12507400-12535200	Weak transcription	Fetal Muscle Leg	muscle
47	chr18:12507800-12518000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:12509400-12539200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr18:12511400-12514800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr18:12511400-12515200	Weak transcription	Adipose Nuclei	Adipose

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