Variant report

Variant	rs17615525
Chromosome Location	chr18:12509095-12509096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12504696..12507292-chr18:12508161..12510716,2	K562	blood:
2	chr18:12491319..12493791-chr18:12507007..12509438,2	K562	blood:
3	chr18:12508980..12512518-chr18:12512927..12516580,4	K562	blood:
4	chr18:12504319..12507292-chr18:12508161..12510811,3	K562	blood:

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1105748	1.00[CHD][hapmap];1.00[LWK][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[ASN][1000 genomes]
rs12957011	1.00[ASN][1000 genomes]
rs12957283	1.00[ASN][1000 genomes]
rs12958301	1.00[ASN][1000 genomes]
rs12959199	1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs12959459	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	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]
rs12961711	1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12964717	1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	1.00[ASN][1000 genomes]
rs12971000	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17524639	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525459	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17525599	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17615801	1.00[CHD][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs17615991	1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs34054541	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34084006	1.00[ASN][1000 genomes]
rs34088731	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34180475	1.00[ASN][1000 genomes]
rs34183067	1.00[ASN][1000 genomes]
rs34215298	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34229934	1.00[ASN][1000 genomes]
rs34371240	1.00[ASN][1000 genomes]
rs34448712	0.91[AFR][1000 genomes]
rs34460164	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34469203	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34512782	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][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	1.00[ASN][1000 genomes]
rs35280383	1.00[ASN][1000 genomes]
rs35309605	1.00[ASN][1000 genomes]
rs35532404	1.00[AFR][1000 genomes];0.88[EUR][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]
rs35872229	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs45541436	1.00[ASN][1000 genomes]
rs559719	1.00[JPT][hapmap]
rs71351482	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351484	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351485	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][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	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs17615525	RP11-861E21.2	cis	Thyroid	GTEx
rs17615525	SLMO1	cis	Esophagus Muscularis	GTEx
rs17615525	SLMO1	cis	Esophagus Mucosa	GTEx
rs17615525	SLMO1	cis	Nerve Tibial	GTEx
rs17615525	AP001029.1	cis	Artery Tibial	GTEx
rs17615525	AP001029.1	cis	Esophagus Muscularis	GTEx
rs17615525	SLMO1	cis	Artery Tibial	GTEx
rs17615525	SLMO1	cis	Thyroid	GTEx
rs17615525	AP001029.1	cis	Thyroid	GTEx
rs17615525	SLMO1	cis	lung	GTEx
rs17615525	SLMO1	cis	Artery Aorta	GTEx
rs17615525	SLMO1	cis	Adipose Subcutaneous	GTEx
rs17615525	RP11-861E21.1	cis	Esophagus Muscularis	GTEx
rs17615525	AP001029.1	cis	Artery Aorta	GTEx

Chromatin state (count:74 , 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	chr18:12478400-12512600	Weak transcription	Fetal Intestine Small	intestine
3	chr18:12478600-12510800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:12478800-12514200	Weak transcription	NH-A	brain
5	chr18:12478800-12515800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr18:12478800-12515800	Weak transcription	Placenta	Placenta
7	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
8	chr18:12480800-12511000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr18:12491600-12510800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr18:12492200-12530400	Weak transcription	HepG2	liver
11	chr18:12492200-12532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr18:12492200-12548600	Weak transcription	Fetal Kidney	kidney
13	chr18:12492400-12515600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr18:12492800-12510800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr18:12493000-12541200	Weak transcription	NHEK	skin
16	chr18:12493200-12510800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:12493200-12512600	Weak transcription	Fetal Brain Male	brain
18	chr18:12493200-12518400	Weak transcription	Esophagus	oesophagus
19	chr18:12493200-12520000	Weak transcription	Colon Smooth Muscle	Colon
20	chr18:12493200-12520400	Weak transcription	Psoas Muscle	Psoas
21	chr18:12493200-12551800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr18:12493400-12515800	Weak transcription	Brain Substantia Nigra	brain
23	chr18:12494000-12515000	Weak transcription	Fetal Lung	lung
24	chr18:12494200-12515000	Weak transcription	HUVEC	blood vessel
25	chr18:12494400-12515600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr18:12495400-12515800	Weak transcription	NHDF-Ad	bronchial
27	chr18:12496000-12515000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr18:12497600-12518000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:12500000-12509200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr18:12500800-12520600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:12502000-12509200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:12502000-12520600	Weak transcription	Fetal Stomach	stomach
33	chr18:12505200-12515800	Weak transcription	Brain Hippocampus Middle	brain
34	chr18:12505200-12516200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr18:12505200-12536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr18:12505400-12509200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr18:12505400-12516000	Weak transcription	Brain Angular Gyrus	brain
38	chr18:12505400-12529400	Weak transcription	HMEC	breast
39	chr18:12505600-12511200	Weak transcription	Lung	lung
40	chr18:12505600-12520000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr18:12505800-12510800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr18:12505800-12510800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr18:12505800-12511000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:12506400-12515600	Weak transcription	Brain Germinal Matrix	brain
45	chr18:12506400-12516000	Weak transcription	Fetal Heart	heart
46	chr18:12506600-12510800	Weak transcription	Adipose Nuclei	Adipose
47	chr18:12506600-12510800	Weak transcription	Ovary	ovary
48	chr18:12506600-12515600	Weak transcription	Brain Anterior Caudate	brain
49	chr18:12506600-12515600	Weak transcription	Left Ventricle	heart
50	chr18:12506600-12516200	Weak transcription	Right Ventricle	heart

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