Variant report

Variant	rs854807
Chromosome Location	chr17:18062443-18062444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
2	chr17:18056639..18059705-chr17:18061625..18064659,3	MCF-7	breast:
3	chr17:18057503..18062681-chr17:18084968..18089396,8	MCF-7	breast:
4	chr17:18061742..18067292-chr17:18083221..18089651,7	K562	blood:
5	chr17:18061892..18063958-chr17:18064455..18066875,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266677	Chromatin interaction
ENSG00000091542	Chromatin interaction
ENSG00000091536	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11869205	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11870766	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11871970	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150618	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12451754	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12936694	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12939469	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12946842	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1378601	0.83[ASN][1000 genomes]
rs1378602	0.83[ASN][1000 genomes]
rs2360234	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2605132	0.89[EUR][1000 genomes]
rs28641923	0.93[ASN][1000 genomes]
rs2925137	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2925138	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4603612	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924839	0.87[ASN][1000 genomes]
rs4924840	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924841	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925149	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925150	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56021431	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712270	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712272	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs712273	0.92[ASN][1000 genomes]
rs712275	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7212808	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8071834	0.90[ASN][1000 genomes]
rs854771	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs854775	0.80[ASN][1000 genomes]
rs854795	0.92[ASN][1000 genomes]
rs854797	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854798	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854799	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs854801	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs854804	0.92[ASN][1000 genomes]
rs854805	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854806	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860567	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs860568	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs861278	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[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	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs854807	ALKBH5	cis	Esophagus Muscularis	GTEx
rs854807	LLGL1	cis	Esophagus Mucosa	GTEx
rs854807	SHMT1	cis	Muscle Skeletal	GTEx
rs854807	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs854807	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs854807	SHMT1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18057600-18063000	Weak transcription	HSMMtube	muscle
2	chr17:18059200-18062600	Enhancers	Spleen	Spleen
3	chr17:18060800-18062600	Weak transcription	A549	lung
4	chr17:18061200-18062600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr17:18061400-18062600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:18062000-18062600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:18062000-18062600	Enhancers	HMEC	breast
8	chr17:18062000-18062800	Enhancers	Left Ventricle	heart
9	chr17:18062000-18062800	Enhancers	Lung	lung
10	chr17:18062000-18063000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr17:18062000-18063000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:18062000-18063400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr17:18062000-18063400	Enhancers	NH-A	brain
14	chr17:18062000-18064400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:18062000-18064800	Weak transcription	Brain Anterior Caudate	brain
16	chr17:18062000-18065800	Enhancers	HSMM	muscle
17	chr17:18062000-18085600	Weak transcription	Brain Angular Gyrus	brain
18	chr17:18062200-18062600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:18062200-18062600	Enhancers	Primary B cells from peripheral blood	blood
20	chr17:18062200-18062600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr17:18062200-18062600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:18062200-18062600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:18062200-18062600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr17:18062200-18062600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr17:18062200-18062600	Enhancers	Ovary	ovary
26	chr17:18062200-18062600	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr17:18062200-18062600	Enhancers	Stomach Mucosa	stomach
28	chr17:18062200-18062800	Enhancers	Pancreas	Pancrea
29	chr17:18062200-18062800	Enhancers	Right Ventricle	heart
30	chr17:18062200-18063000	Weak transcription	Liver	Liver
31	chr17:18062200-18063200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr17:18062200-18063400	Enhancers	Fetal Intestine Large	intestine
33	chr17:18062200-18063400	Enhancers	Fetal Intestine Small	intestine
34	chr17:18062200-18063400	Enhancers	Placenta	Placenta
35	chr17:18062200-18063600	Enhancers	Muscle Satellite Cultured Cells	--
36	chr17:18062200-18063600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr17:18062200-18063600	Enhancers	NHDF-Ad	bronchial
38	chr17:18062200-18063600	Enhancers	NHLF	lung
39	chr17:18062200-18063600	Enhancers	Osteobl	bone
40	chr17:18062200-18063800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr17:18062200-18064600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:18062200-18065200	Enhancers	Fetal Muscle Leg	muscle
43	chr17:18062200-18065400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr17:18062200-18066600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr17:18062200-18067600	Enhancers	K562	blood
46	chr17:18062200-18085000	Weak transcription	Right Atrium	heart
47	chr17:18062400-18062600	Enhancers	Primary T cells fromperipheralblood	blood
48	chr17:18062400-18062600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr17:18062400-18062800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr17:18062400-18062800	Enhancers	Fetal Muscle Trunk	muscle

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