Variant report

Variant	rs9846089
Chromosome Location	chr3:52529773-52529774
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52517051..52518693-chr3:52528843..52530538,2	K562	blood:
2	chr3:52488362..52490407-chr3:52528579..52530282,2	K562	blood:
3	chr3:52527250..52529955-chr3:52567199..52569414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010322	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1011062	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1011063	1.00[JPT][hapmap]
rs1011064	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1035002	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1035003	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs10865972	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs123598	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs123602	1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap]
rs13074649	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[JPT][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs13096571	0.80[EUR][1000 genomes]
rs1541495	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	1.00[JPT][hapmap]
rs2109557	0.88[EUR][1000 genomes]
rs2109558	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2109559	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2159607	1.00[JPT][hapmap]
rs2215466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2335929	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2878549	1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs35860312	1.00[JPT][hapmap]
rs3755810	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774409	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs390802	1.00[JPT][hapmap]
rs409803	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs41292858	1.00[AFR][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs419752	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4312651	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687541	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687543	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4687544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687545	1.00[AFR][1000 genomes]
rs4687614	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687616	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4687617	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687618	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687619	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs498778	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs498946	1.00[JPT][hapmap]
rs575476	0.88[EUR][1000 genomes]
rs613519	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs634382	1.00[JPT][hapmap]
rs6414568	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445483	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445485	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445486	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445506	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs676034	1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784615	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787493	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795333	0.81[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap]
rs6810027	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728408	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs758800	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs758802	1.00[AFR][1000 genomes]
rs758803	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7620015	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs887515	1.00[JPT][hapmap]
rs929528	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929529	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9847332	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9850471	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9855470	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863753	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867823	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9846089	TMEM110	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52508000-52532200	Weak transcription	K562	blood
2	chr3:52513400-52541400	Weak transcription	A549	lung
3	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
4	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
5	chr3:52519400-52530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:52521000-52529800	Weak transcription	Hela-S3	cervix
7	chr3:52526000-52530200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52527000-52530000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:52527000-52530200	Weak transcription	HSMMtube	muscle
10	chr3:52527000-52532400	Weak transcription	GM12878-XiMat	blood
11	chr3:52527000-52538000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:52527000-52540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52527200-52530400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:52527200-52531200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:52527400-52529800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:52527400-52530600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:52527400-52532600	Weak transcription	Stomach Mucosa	stomach
18	chr3:52527600-52530400	Weak transcription	Dnd41	blood
19	chr3:52527800-52531600	Weak transcription	Primary B cells from cord blood	blood
20	chr3:52527800-52531800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:52527800-52532800	Weak transcription	Primary T cells from cord blood	blood
22	chr3:52527800-52533200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:52527800-52533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52528000-52529800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:52528000-52532000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:52528000-52534800	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:52528200-52529800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr3:52528400-52529800	Enhancers	Fetal Thymus	thymus
29	chr3:52528600-52529800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:52528600-52530400	Weak transcription	Brain Germinal Matrix	brain
31	chr3:52528600-52530600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:52528600-52533600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr3:52528800-52530000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:52528800-52530000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:52528800-52530400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:52528800-52530400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:52528800-52530400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:52528800-52530800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:52528800-52530800	Active TSS	Rectal Smooth Muscle	rectum
40	chr3:52528800-52531000	Active TSS	Duodenum Mucosa	Duodenum
41	chr3:52529000-52529800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr3:52529000-52530200	Active TSS	Stomach Smooth Muscle	stomach
43	chr3:52529000-52530800	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:52529000-52530800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr3:52529000-52531000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
46	chr3:52529200-52529800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:52529200-52529800	Flanking Active TSS	Right Atrium	heart
48	chr3:52529200-52530000	Active TSS	Placenta	Placenta
49	chr3:52529200-52530200	Enhancers	NH-A	brain
50	chr3:52529200-52531200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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