Variant report

Variant	rs10164125
Chromosome Location	chr18:12410278-12410279
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12374593..12378692-chr18:12406477..12410976,5	K562	blood:
2	chr18:12407594..12413164-chr18:12414407..12422412,12	MCF-7	breast:
3	chr18:12410197..12415577-chr18:12418474..12421681,6	MCF-7	breast:
4	chr18:12406559..12410304-chr18:12656888..12659730,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141391	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11662125	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs11662659	0.93[CEU][hapmap];0.87[AMR][1000 genomes]
rs11665192	0.89[CEU][hapmap];0.82[AMR][1000 genomes]
rs12967213	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16977182	0.93[CEU][hapmap]
rs16977185	0.93[CEU][hapmap]
rs2096847	0.93[CEU][hapmap]
rs4797681	0.80[AMR][1000 genomes]
rs58493287	0.80[AMR][1000 genomes]
rs7242792	0.93[CEU][hapmap];0.83[AMR][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	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	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10164125	SLMO1	cis	Adipose Subcutaneous	GTEx
rs10164125	TUBB6	cis	Whole Blood	GTEx
rs10164125	AP001029.1	cis	Esophagus Muscularis	GTEx
rs10164125	SLMO1	cis	Artery Tibial	GTEx
rs10164125	SLMO1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12408600-12410600	Enhancers	Fetal Heart	heart
2	chr18:12408600-12419600	Weak transcription	Thymus	Thymus
3	chr18:12408800-12410400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr18:12408800-12410400	Enhancers	Lung	lung
5	chr18:12408800-12410600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr18:12408800-12410800	Weak transcription	Placenta	Placenta
7	chr18:12408800-12415000	Weak transcription	Ovary	ovary
8	chr18:12408800-12415600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:12408800-12415600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:12408800-12415800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr18:12408800-12415800	Weak transcription	Left Ventricle	heart
12	chr18:12408800-12417800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr18:12408800-12419800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr18:12408800-12419800	Weak transcription	Pancreas	Pancrea
15	chr18:12409000-12410600	Enhancers	Brain Cingulate Gyrus	brain
16	chr18:12409000-12410600	Enhancers	Brain Substantia Nigra	brain
17	chr18:12409000-12410600	Enhancers	Osteobl	bone
18	chr18:12409000-12410800	Enhancers	Fetal Muscle Leg	muscle
19	chr18:12409000-12411000	Enhancers	Fetal Muscle Trunk	muscle
20	chr18:12409000-12411200	Enhancers	K562	blood
21	chr18:12409000-12411600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr18:12409000-12414000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr18:12409000-12414000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr18:12409000-12415800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr18:12409000-12415800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr18:12409000-12415800	Weak transcription	Fetal Intestine Small	intestine
27	chr18:12409000-12415800	Weak transcription	Fetal Lung	lung
28	chr18:12409000-12416000	Weak transcription	Aorta	Aorta
29	chr18:12409000-12416000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:12409000-12417600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr18:12409000-12419600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr18:12409000-12419800	Weak transcription	Colonic Mucosa	Colon
33	chr18:12409000-12419800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr18:12409000-12419800	Weak transcription	Fetal Kidney	kidney
35	chr18:12409000-12419800	Weak transcription	Fetal Thymus	thymus
36	chr18:12409200-12410400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:12409200-12410600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr18:12409200-12410600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:12409200-12410600	Enhancers	HMEC	breast
40	chr18:12409200-12410600	Enhancers	HUVEC	blood vessel
41	chr18:12409200-12414000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr18:12409200-12414200	Weak transcription	Brain Anterior Caudate	brain
43	chr18:12409200-12415600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr18:12409200-12415800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr18:12409200-12418400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr18:12409400-12410400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr18:12409400-12410600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr18:12409400-12410600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr18:12409600-12410400	Enhancers	Right Ventricle	heart
50	chr18:12409600-12410600	Enhancers	Brain Inferior Temporal Lobe	brain

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