Variant report

Variant	rs11874852
Chromosome Location	chr18:12520278-12520279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr18:12520126-12521155	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12512543..12514903-chr18:12518908..12520482,2	MCF-7	breast:
2	chr18:12519825..12522485-chr18:12525677..12527572,2	K562	blood:

Variant related genes	Relation type
SPIRE1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12457026	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs12457771	0.83[CEU][hapmap]
rs12960623	0.84[JPT][hapmap]
rs12968771	0.86[JPT][hapmap]
rs1549011	0.81[JPT][hapmap]
rs17616402	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs3902981	0.81[JPT][hapmap]
rs55634668	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs566326	0.92[CEU][hapmap]
rs57010148	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7229168	1.00[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7233175	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs9303774	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11874852	TNFSF5IP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12478800-12551800	Weak transcription	Pancreas	Pancrea
2	chr18:12492200-12530400	Weak transcription	HepG2	liver
3	chr18:12492200-12532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr18:12492200-12548600	Weak transcription	Fetal Kidney	kidney
5	chr18:12493000-12541200	Weak transcription	NHEK	skin
6	chr18:12493200-12520400	Weak transcription	Psoas Muscle	Psoas
7	chr18:12493200-12551800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr18:12500800-12520600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr18:12502000-12520600	Weak transcription	Fetal Stomach	stomach
10	chr18:12505200-12536800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:12505400-12529400	Weak transcription	HMEC	breast
12	chr18:12507000-12526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:12507400-12535200	Weak transcription	Fetal Muscle Leg	muscle
14	chr18:12509400-12539200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr18:12511400-12521600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr18:12511400-12551800	Weak transcription	Lung	lung
17	chr18:12511800-12520400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr18:12511800-12520600	Weak transcription	HSMMtube	muscle
19	chr18:12514600-12522000	Enhancers	Fetal Brain Male	brain
20	chr18:12515600-12521400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr18:12516000-12553200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:12516400-12520400	Weak transcription	Brain Angular Gyrus	brain
23	chr18:12516400-12520400	Weak transcription	NHLF	lung
24	chr18:12516400-12539000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr18:12516600-12520600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:12516600-12520800	Weak transcription	Left Ventricle	heart
27	chr18:12516600-12529400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr18:12516600-12536600	Weak transcription	Right Ventricle	heart
29	chr18:12516600-12555000	Weak transcription	Aorta	Aorta
30	chr18:12516800-12520400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr18:12516800-12520400	Weak transcription	Fetal Heart	heart
32	chr18:12516800-12524600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr18:12516800-12534400	Weak transcription	HUVEC	blood vessel
34	chr18:12517000-12520600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr18:12517200-12520400	Weak transcription	Brain Substantia Nigra	brain
36	chr18:12518200-12520400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr18:12518400-12520600	Weak transcription	Ovary	ovary
38	chr18:12518400-12530200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr18:12518600-12520400	Enhancers	Fetal Brain Female	brain
40	chr18:12518600-12531200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr18:12518600-12540000	Weak transcription	Adipose Nuclei	Adipose
42	chr18:12518600-12551800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr18:12519000-12532800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:12519200-12521600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr18:12519400-12520400	Weak transcription	Fetal Lung	lung
46	chr18:12519400-12521200	Enhancers	Brain Germinal Matrix	brain
47	chr18:12519400-12521600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12519600-12520600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr18:12519600-12520800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr18:12519600-12520800	Enhancers	Pancreatic Islets	Pancreatic Islet

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