Variant report

Variant	rs71351485
Chromosome Location	chr18:12492916-12492917
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12492408..12492934-chr2:36835622..36836122,2	Hela-S3	cervix:
2	chr18:12487888..12489468-chr18:12491186..12492956,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1105748	1.00[ASN][1000 genomes]
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[ASN][1000 genomes]
rs12959459	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12959998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12961307	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12963149	1.00[ASN][1000 genomes]
rs12967250	1.00[ASN][1000 genomes]
rs12970939	1.00[ASN][1000 genomes]
rs12971000	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17524639	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525318	1.00[ASN][1000 genomes]
rs17525459	1.00[ASN][1000 genomes]
rs17525599	1.00[ASN][1000 genomes]
rs17615525	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17615801	1.00[ASN][1000 genomes]
rs17615991	1.00[ASN][1000 genomes]
rs17616124	1.00[ASN][1000 genomes]
rs1977937	0.83[EUR][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];0.86[AMR][1000 genomes];0.96[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];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34460164	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34469203	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34503700	1.00[ASN][1000 genomes]
rs34512782	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34620743	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34737110	1.00[ASN][1000 genomes]
rs34859829	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];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35612342	1.00[ASN][1000 genomes]
rs35744165	1.00[ASN][1000 genomes]
rs35815040	1.00[ASN][1000 genomes]
rs35826479	1.00[ASN][1000 genomes]
rs35872229	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35939870	1.00[ASN][1000 genomes]
rs4510091	1.00[ASN][1000 genomes]
rs71351482	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71351484	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[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]
rs71363149	1.00[ASN][1000 genomes]
rs919	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
rs71351485	SLMO1	cis	Esophagus Mucosa	GTEx
rs71351485	SLMO1	cis	lung	GTEx
rs71351485	RP11-861E21.1	cis	Esophagus Muscularis	GTEx
rs71351485	AP001029.1	cis	Esophagus Muscularis	GTEx
rs71351485	AP001029.1	cis	Thyroid	GTEx
rs71351485	RP11-861E21.1	cis	Artery Tibial	GTEx
rs71351485	SLMO1	cis	Thyroid	GTEx
rs71351485	SLMO1	cis	Artery Tibial	GTEx
rs71351485	SLMO1	cis	Artery Aorta	GTEx
rs71351485	SLMO1	cis	Esophagus Muscularis	GTEx
rs71351485	AP001029.1	cis	Artery Tibial	GTEx
rs71351485	SLMO1	cis	Adipose Subcutaneous	GTEx
rs71351485	SLMO1	cis	Nerve Tibial	GTEx
rs71351485	AP001029.1	cis	Artery Aorta	GTEx

Chromatin state (count:86 , 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	chr18:12461400-12495400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr18:12465600-12500800	Weak transcription	Fetal Intestine Large	intestine
4	chr18:12472600-12495200	Weak transcription	Colonic Mucosa	Colon
5	chr18:12478400-12512600	Weak transcription	Fetal Intestine Small	intestine
6	chr18:12478600-12496000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:12478600-12498400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr18:12478600-12506400	Weak transcription	Right Ventricle	heart
9	chr18:12478600-12510800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr18:12478800-12497400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:12478800-12499600	Weak transcription	NHLF	lung
12	chr18:12478800-12504800	Weak transcription	Gastric	stomach
13	chr18:12478800-12505800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr18:12478800-12514200	Weak transcription	NH-A	brain
15	chr18:12478800-12515800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:12478800-12515800	Weak transcription	Placenta	Placenta
17	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
18	chr18:12480800-12497200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr18:12480800-12511000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr18:12481000-12499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr18:12484000-12496200	Strong transcription	HSMM	muscle
22	chr18:12486200-12504600	Weak transcription	HMEC	breast
23	chr18:12488000-12496000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:12488400-12496200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:12490200-12503400	Weak transcription	Brain Angular Gyrus	brain
26	chr18:12490400-12496000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr18:12490400-12502800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr18:12490800-12494000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr18:12490800-12494000	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr18:12491000-12496400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr18:12491200-12493200	Strong transcription	Liver	Liver
32	chr18:12491200-12494000	Weak transcription	A549	lung
33	chr18:12491200-12495800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr18:12491200-12495800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr18:12491400-12493000	Strong transcription	NHEK	skin
36	chr18:12491400-12493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr18:12491400-12493200	Strong transcription	Left Ventricle	heart
38	chr18:12491400-12493200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr18:12491400-12493400	Strong transcription	Adipose Nuclei	Adipose
40	chr18:12491400-12493400	Strong transcription	Ovary	ovary
41	chr18:12491400-12493800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr18:12491400-12494000	Strong transcription	Fetal Lung	lung
43	chr18:12491400-12494200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:12491400-12494200	Strong transcription	Brain Anterior Caudate	brain
45	chr18:12491400-12494400	Strong transcription	Brain Germinal Matrix	brain
46	chr18:12491400-12494600	Strong transcription	Fetal Muscle Leg	muscle
47	chr18:12491400-12494600	Strong transcription	NHDF-Ad	bronchial
48	chr18:12491400-12495400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr18:12491400-12496000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr18:12491400-12496000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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