Variant report

Variant	rs1893217
Chromosome Location	chr18:12809340-12809341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12808897..12811465-chr18:12881476..12883993,2	MCF-7	breast:
2	chr18:12805583..12807776-chr18:12809327..12811664,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11663253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014857	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2542147	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542148	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542149	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542150	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2542151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847259	0.91[ASN][1000 genomes]
rs2847260	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847274	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847278	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847280	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2847293	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34920518	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45450798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60474474	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60735058	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60751993	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7237497	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8096138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064273	chr18:12697601-12828251	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
8	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

Variant related diseases (count:5)

Disease	PMID	Source
Inflammatory bowel disease	23128233	GWAS catalog
Type 1 diabetes	19430480	GWAS catalog
Crohn's disease	21102463	GWAS catalog
Celiac disease or Rheumatoid arthritis	21383967	GWAS catalog
Celiac disease	20190752	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1893217	RP11-973H7.1	cis	Esophagus Muscularis	GTEx
rs1893217	ZNF283	trans	parietal	SCAN
rs1893217	RP11-973H7.1	cis	Artery Tibial	GTEx
rs1893217	RP11-973H7.1	cis	lung	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12767400-12815800	Weak transcription	Gastric	stomach
2	chr18:12776800-12819800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
4	chr18:12782000-12811200	Weak transcription	Right Ventricle	heart
5	chr18:12787600-12815800	Weak transcription	Pancreas	Pancrea
6	chr18:12789000-12821400	Weak transcription	Small Intestine	intestine
7	chr18:12789200-12814200	Weak transcription	Fetal Kidney	kidney
8	chr18:12790200-12828000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr18:12790400-12813600	Weak transcription	A549	lung
10	chr18:12790400-12814000	Weak transcription	Osteobl	bone
11	chr18:12790400-12815800	Weak transcription	K562	blood
12	chr18:12790600-12820000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr18:12791200-12815800	Weak transcription	Brain Germinal Matrix	brain
14	chr18:12791200-12819600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr18:12791400-12819600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
17	chr18:12791600-12828000	Weak transcription	HUVEC	blood vessel
18	chr18:12791800-12821600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr18:12792200-12815800	Weak transcription	NH-A	brain
20	chr18:12792800-12815800	Weak transcription	Brain Angular Gyrus	brain
21	chr18:12792800-12819600	Weak transcription	NHLF	lung
22	chr18:12793000-12811400	Strong transcription	Fetal Thymus	thymus
23	chr18:12794600-12815800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr18:12795200-12815800	Weak transcription	Brain Anterior Caudate	brain
25	chr18:12797800-12819800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr18:12798000-12814800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr18:12798200-12814200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr18:12798200-12814200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr18:12801200-12815600	Weak transcription	HepG2	liver
30	chr18:12801400-12810400	Weak transcription	HMEC	breast
31	chr18:12801400-12813600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr18:12801800-12812400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr18:12801800-12815600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr18:12802000-12811200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr18:12802200-12812200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr18:12802200-12813200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr18:12802200-12814400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr18:12802400-12812600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr18:12803600-12813200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr18:12804000-12813800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr18:12804000-12814200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr18:12805000-12812800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr18:12806400-12816600	Strong transcription	Primary B cells from cord blood	blood
45	chr18:12806400-12827600	Strong transcription	Dnd41	blood
46	chr18:12806800-12827400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr18:12807000-12811200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr18:12807000-12811600	Weak transcription	Fetal Intestine Large	intestine
49	chr18:12807000-12815400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr18:12807000-12815600	Weak transcription	Fetal Brain Female	brain

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