Variant report

Variant	rs12455948
Chromosome Location	chr18:12414326-12414327
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	chr18:12410197..12415577-chr18:12418474..12421681,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141391	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12454554	0.82[ASN][1000 genomes]
rs12956344	0.84[CEU][hapmap]
rs546713	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71351477	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7243316	0.85[CEU][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs72875353	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv909404	chr18:12409955-12438402	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12455948	PSMG2	cis	parietal	SCAN
rs12455948	SPIRE1	cis	lymphoblastoid	seeQTL
rs12455948	TUBB6	cis	lymphoblastoid	seeQTL
rs12455948	SLMO1	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12408600-12419600	Weak transcription	Thymus	Thymus
2	chr18:12408800-12415000	Weak transcription	Ovary	ovary
3	chr18:12408800-12415600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:12408800-12415600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr18:12408800-12415800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:12408800-12415800	Weak transcription	Left Ventricle	heart
7	chr18:12408800-12417800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:12408800-12419800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr18:12408800-12419800	Weak transcription	Pancreas	Pancrea
10	chr18:12409000-12415800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:12409000-12415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr18:12409000-12415800	Weak transcription	Fetal Intestine Small	intestine
13	chr18:12409000-12415800	Weak transcription	Fetal Lung	lung
14	chr18:12409000-12416000	Weak transcription	Aorta	Aorta
15	chr18:12409000-12416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr18:12409000-12417600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr18:12409000-12419600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr18:12409000-12419800	Weak transcription	Colonic Mucosa	Colon
19	chr18:12409000-12419800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr18:12409000-12419800	Weak transcription	Fetal Kidney	kidney
21	chr18:12409000-12419800	Weak transcription	Fetal Thymus	thymus
22	chr18:12409200-12415600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr18:12409200-12415800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:12409200-12418400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr18:12409800-12415600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr18:12409800-12418000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:12409800-12419800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr18:12410000-12415600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:12410000-12415600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr18:12410200-12419800	Weak transcription	NH-A	brain
31	chr18:12410400-12415600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr18:12410400-12415600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr18:12410400-12415600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:12410400-12415600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr18:12410400-12415800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr18:12410400-12417200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:12410400-12419800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr18:12410400-12419800	Weak transcription	Right Ventricle	heart
39	chr18:12410400-12430400	Weak transcription	A549	lung
40	chr18:12410600-12414400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:12410600-12415000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:12410600-12415000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr18:12410600-12415000	Weak transcription	HSMMtube	muscle
44	chr18:12410600-12415000	Weak transcription	NHDF-Ad	bronchial
45	chr18:12410600-12415400	Weak transcription	HSMM	muscle
46	chr18:12410600-12415600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr18:12410600-12415600	Weak transcription	HUVEC	blood vessel
48	chr18:12410600-12415600	Weak transcription	NHLF	lung
49	chr18:12410600-12415600	Weak transcription	Osteobl	bone
50	chr18:12410600-12415800	Weak transcription	Fetal Heart	heart

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