Variant report

Variant	rs35643817
Chromosome Location	chr18:12448877-12448878
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	chr18:12431522..12433489-chr18:12448330..12450426,2	MCF-7	breast:
2	chr18:12448427..12450836-chr18:12453121..12454748,2	K562	blood:

Variant related genes	Relation type
ENSG00000256786	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000267108	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12957885	1.00[AFR][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	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	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs35643817	SPIRE1	Cis_1M	lymphoblastoid	RTeQTL
rs35643817	AP001029.1	cis	Esophagus Muscularis	GTEx
rs35643817	SLMO1	cis	Artery Tibial	GTEx
rs35643817	AP001029.1	cis	Thyroid	GTEx
rs35643817	SLMO1	cis	Esophagus Muscularis	GTEx
rs35643817	SLMO1	cis	Thyroid	GTEx
rs35643817	SLMO1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
3	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
4	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr18:12433200-12449200	Weak transcription	Gastric	stomach
6	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
7	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
8	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr18:12433400-12458600	Weak transcription	HepG2	liver
10	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
11	chr18:12435200-12449000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr18:12438200-12449200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr18:12439400-12468200	Weak transcription	K562	blood
14	chr18:12441600-12452200	Weak transcription	Hela-S3	cervix
15	chr18:12442000-12459200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:12443200-12457400	Strong transcription	HSMM	muscle
17	chr18:12443600-12454600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr18:12444000-12449000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr18:12444000-12460200	Weak transcription	Fetal Intestine Large	intestine
20	chr18:12444000-12467400	Weak transcription	A549	lung
21	chr18:12444200-12463200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr18:12444400-12453400	Weak transcription	Small Intestine	intestine
23	chr18:12444400-12458600	Weak transcription	Fetal Heart	heart
24	chr18:12444400-12465800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr18:12444600-12449000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:12444600-12449000	Weak transcription	Brain Anterior Caudate	brain
27	chr18:12444600-12449200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr18:12444600-12450200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr18:12444600-12455800	Weak transcription	Fetal Kidney	kidney
30	chr18:12444600-12457600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr18:12444600-12459400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr18:12444600-12477600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr18:12444800-12449000	Weak transcription	Right Ventricle	heart
34	chr18:12444800-12450400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr18:12444800-12450800	Strong transcription	Fetal Brain Female	brain
36	chr18:12445000-12450000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr18:12445000-12454800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr18:12445600-12449000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12445600-12459200	Weak transcription	Fetal Intestine Small	intestine
40	chr18:12445600-12460800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr18:12445800-12449000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr18:12445800-12449000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr18:12445800-12449000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr18:12445800-12449000	Weak transcription	Ovary	ovary
45	chr18:12445800-12449200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr18:12445800-12459000	Weak transcription	Placenta	Placenta
47	chr18:12446200-12479600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr18:12446600-12452000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr18:12446800-12450000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr18:12446800-12452800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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