Variant report

Variant	rs11718060
Chromosome Location	chr3:52875546-52875547
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	RUNX3	chr3:52875142-52875651	GM12878	blood:	n/a	n/a
2	TCF12	chr3:52875285-52875552	GM12878	blood:	n/a	chr3:52875440-52875448

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52803715..52805902-chr3:52874029..52875964,2	MCF-7	breast:

Variant related genes	Relation type
TMEM110-MUSTN1	TF binding region
TMEM110	TF binding region
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130329	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1139106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707829	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11708390	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes]
rs11709430	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712498	1.00[CHB][hapmap]
rs11713324	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs11717749	1.00[CHB][hapmap]
rs11720228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11720233	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs13067373	0.81[CEU][hapmap]
rs13076033	1.00[CHB][hapmap]
rs13080929	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17331151	1.00[CHB][hapmap]
rs17331178	1.00[CHB][hapmap]
rs1986656	0.81[CEU][hapmap]
rs2001732	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071039	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2240916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276818	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276822	1.00[JPT][hapmap]
rs2336661	0.81[CEU][hapmap]
rs28552648	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33999310	1.00[ASN][1000 genomes]
rs34288509	1.00[ASN][1000 genomes]
rs34860124	1.00[ASN][1000 genomes]
rs3755801	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755805	0.92[ASN][1000 genomes]
rs3796352	1.00[CHB][hapmap]
rs4687556	0.91[EUR][1000 genomes]
rs4687676	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798472	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs9637477	0.93[EUR][1000 genomes]
rs9831977	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv967253	chr3:52871714-52877079	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11718060	TMEM110	cis	multi-tissue	Pritchard
rs11718060	TMEM110	cis	Thyroid	GTEx
rs11718060	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
5	chr3:52866000-52884800	Weak transcription	HMEC	breast
6	chr3:52866200-52885200	Weak transcription	NHEK	skin
7	chr3:52866600-52879200	Weak transcription	Osteobl	bone
8	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
10	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
11	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
17	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:52869000-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:52869000-52879400	Strong transcription	Fetal Intestine Small	intestine
20	chr3:52869000-52881800	Weak transcription	Fetal Kidney	kidney
21	chr3:52869400-52875600	Weak transcription	Colonic Mucosa	Colon
22	chr3:52869600-52878600	Weak transcription	NHDF-Ad	bronchial
23	chr3:52869600-52879600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:52869600-52881800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:52869800-52875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:52869800-52876600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:52869800-52882000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:52869800-52884000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:52870000-52878800	Genic enhancers	Fetal Muscle Leg	muscle
30	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
31	chr3:52870200-52875600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr3:52870200-52876600	Strong transcription	Fetal Stomach	stomach
33	chr3:52870400-52875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:52870400-52876400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:52870400-52877400	Strong transcription	Lung	lung
36	chr3:52870600-52877000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:52870600-52877400	Strong transcription	Adipose Nuclei	Adipose
38	chr3:52870600-52879400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:52871200-52879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:52871600-52876600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:52871600-52877600	Strong transcription	Brain Hippocampus Middle	brain
42	chr3:52872200-52875600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr3:52872200-52878800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:52872400-52876800	Strong transcription	Aorta	Aorta
45	chr3:52872400-52877000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:52872400-52877000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:52872600-52876000	Strong transcription	Colon Smooth Muscle	Colon
48	chr3:52872600-52876600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:52872600-52876600	Strong transcription	Brain Substantia Nigra	brain
50	chr3:52872600-52877000	Strong transcription	Ovary	ovary

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