Variant report

Variant	rs9954419
Chromosome Location	chr18:12608220-12608221
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12603548..12606343-chr18:12607471..12609019,2	K562	blood:
2	chr18:12595958..12597985-chr18:12607168..12608800,2	MCF-7	breast:
3	chr18:12601083..12604521-chr18:12605372..12609062,5	MCF-7	breast:

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10401097	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11080585	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11080586	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11080590	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11659510	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11659854	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11663958	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11664404	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11664765	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11664861	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11664914	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11664917	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11664927	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11664936	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11665543	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12326271	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12454931	0.85[ASN][1000 genomes]
rs12455536	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12455892	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12455909	0.88[ASN][1000 genomes]
rs12604184	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12604385	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12604400	0.80[ASN][1000 genomes]
rs12604402	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12604541	0.87[ASN][1000 genomes]
rs12605240	0.87[ASN][1000 genomes]
rs12605392	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12606465	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12606482	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12606506	0.84[ASN][1000 genomes]
rs12709540	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12953578	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12956133	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12956385	0.83[ASN][1000 genomes]
rs12956885	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12957048	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12957151	0.80[AFR][1000 genomes]
rs12957688	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12958200	0.85[ASN][1000 genomes]
rs12959015	0.84[ASN][1000 genomes]
rs12960150	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12961695	0.83[ASN][1000 genomes]
rs12962476	0.88[ASN][1000 genomes]
rs12963179	0.83[ASN][1000 genomes]
rs12963325	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12965094	0.84[ASN][1000 genomes]
rs12969567	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12970025	0.88[ASN][1000 genomes]
rs1864532	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1893193	0.83[ASN][1000 genomes]
rs1940974	0.87[ASN][1000 genomes]
rs1940975	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2155698	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2186907	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28414067	0.87[ASN][1000 genomes]
rs28457089	0.82[ASN][1000 genomes]
rs28496036	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs28582228	0.88[ASN][1000 genomes]
rs28647784	0.82[ASN][1000 genomes]
rs28886423	0.88[ASN][1000 genomes]
rs34072260	0.84[ASN][1000 genomes]
rs34814556	0.82[ASN][1000 genomes]
rs34899007	0.84[ASN][1000 genomes]
rs35122110	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35449211	0.84[ASN][1000 genomes]
rs35630805	0.89[ASN][1000 genomes]
rs4389196	0.88[ASN][1000 genomes]
rs4627434	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4629035	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62097094	0.83[ASN][1000 genomes]
rs62097126	0.87[ASN][1000 genomes]
rs62097148	0.89[ASN][1000 genomes]
rs62097149	0.87[ASN][1000 genomes]
rs62097152	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62097153	0.87[ASN][1000 genomes]
rs67045810	0.87[ASN][1000 genomes]
rs70964152	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs722708	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7234697	0.83[ASN][1000 genomes]
rs7237732	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7238080	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs723836	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7238546	0.87[ASN][1000 genomes]
rs7242395	0.83[ASN][1000 genomes]
rs7504857	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs755020	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs755021	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8086094	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8087885	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8088786	0.87[ASN][1000 genomes]
rs8089081	0.82[ASN][1000 genomes]
rs8089115	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8093129	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8093532	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8094172	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8095160	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8096455	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303772	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303773	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs948301	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs948302	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs948303	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9675543	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9710023	0.81[ASN][1000 genomes]
rs9945339	0.88[ASN][1000 genomes]
rs9947738	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9948505	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9948618	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9949582	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9951147	0.87[ASN][1000 genomes]
rs9954054	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9958409	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9958666	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9959759	0.87[ASN][1000 genomes]
rs9960824	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9961705	0.84[ASN][1000 genomes]
rs9961851	0.88[ASN][1000 genomes]
rs9964759	0.89[ASN][1000 genomes]
rs9965123	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9967123	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9989496	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9989506	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9989568	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9954419	SLMO1,HMGB3	cis	brain	BrainEAC

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12597800-12610800	Weak transcription	Right Ventricle	heart
2	chr18:12597800-12634600	Weak transcription	Aorta	Aorta
3	chr18:12598000-12610000	Weak transcription	Lung	lung
4	chr18:12598600-12608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr18:12598800-12609000	Weak transcription	Right Atrium	heart
6	chr18:12600400-12608600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr18:12602200-12609200	Weak transcription	Fetal Brain Male	brain
8	chr18:12602200-12638400	Weak transcription	Fetal Brain Female	brain
9	chr18:12602800-12611200	Weak transcription	Spleen	Spleen
10	chr18:12604800-12610800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr18:12605800-12609200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr18:12605800-12609600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:12605800-12609800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr18:12606000-12610800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:12606000-12615600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:12606200-12610000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr18:12606200-12616200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr18:12606400-12609400	Enhancers	Osteobl	bone
19	chr18:12606400-12609600	Enhancers	HMEC	breast
20	chr18:12606600-12608800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr18:12606600-12609200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr18:12606600-12611600	Enhancers	HepG2	liver
23	chr18:12606800-12609000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr18:12606800-12609000	Enhancers	HSMM	muscle
25	chr18:12606800-12609200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr18:12606800-12609200	Enhancers	Brain Anterior Caudate	brain
27	chr18:12606800-12609400	Enhancers	Brain Hippocampus Middle	brain
28	chr18:12607000-12609200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr18:12607000-12609200	Enhancers	Brain Substantia Nigra	brain
30	chr18:12607000-12609200	Enhancers	NHLF	lung
31	chr18:12607000-12609800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr18:12607000-12640200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr18:12607200-12608800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr18:12607400-12608800	Enhancers	NH-A	brain
35	chr18:12607400-12615600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr18:12607400-12616000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:12607600-12608400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr18:12607600-12608600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr18:12607600-12609000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr18:12607600-12609200	Enhancers	NHDF-Ad	bronchial
41	chr18:12607600-12609600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr18:12607600-12610600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr18:12607800-12608800	Enhancers	A549	lung
44	chr18:12607800-12609200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr18:12607800-12609200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:12607800-12609400	Enhancers	Hela-S3	cervix
47	chr18:12607800-12609400	Enhancers	HUVEC	blood vessel
48	chr18:12607800-12609400	Enhancers	NHEK	skin
49	chr18:12607800-12609800	Weak transcription	K562	blood
50	chr18:12607800-12610200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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