Variant report

Variant	rs7123861
Chromosome Location	chr11:8892323-8892324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8706918..8709095-chr11:8891415..8893255,2	MCF-7	breast:
2	chr11:8891163..8893518-chr11:8931818..8934397,2	MCF-7	breast:
3	chr11:8701293..8704221-chr11:8890079..8892942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction
ENSG00000166452	Chromatin interaction
ENSG00000212607	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10743093	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10743095	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10769967	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10769968	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769970	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769971	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769973	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10840130	0.82[EUR][1000 genomes]
rs10840134	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10840136	0.81[EUR][1000 genomes]
rs10840141	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840142	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10840147	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840148	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042078	0.82[EUR][1000 genomes]
rs11042079	0.82[EUR][1000 genomes]
rs11042082	0.84[EUR][1000 genomes]
rs11042088	0.84[EUR][1000 genomes]
rs11042102	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042103	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042125	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1109305	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11603841	0.84[EUR][1000 genomes]
rs1529641	0.85[EUR][1000 genomes]
rs1560569	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1569408	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1883098	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1988708	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1988709	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2016942	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568043	0.85[EUR][1000 genomes]
rs2568054	0.95[EUR][1000 genomes]
rs2568059	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568061	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568062	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568065	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568090	0.84[EUR][1000 genomes]
rs2653567	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2653593	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653606	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2653607	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2653613	0.81[EUR][1000 genomes]
rs2653616	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742537	0.82[EUR][1000 genomes]
rs2742540	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2742545	0.81[EUR][1000 genomes]
rs2742550	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2742552	0.81[EUR][1000 genomes]
rs34842234	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36192694	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4554887	0.84[EUR][1000 genomes]
rs4909952	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910062	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4910119	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910156	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910157	0.84[ASN][1000 genomes]
rs4910158	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910200	0.84[EUR][1000 genomes]
rs61876187	0.84[EUR][1000 genomes]
rs7118463	0.80[EUR][1000 genomes]
rs7119939	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7123429	0.92[EUR][1000 genomes]
rs7937298	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7943377	0.83[EUR][1000 genomes]
rs978636	0.84[EUR][1000 genomes]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	esv3402630	chr11:8887304-8893757	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3325077	chr11:8887314-8893755	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7123861	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs7123861	AKIP1	cis	Thyroid	GTEx
rs7123861	TMEM9B-AS1	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8890800-8893000	Active TSS	NHLF	lung
2	chr11:8891000-8893200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:8891000-8893200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr11:8891200-8893600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:8891400-8893000	Active TSS	Fetal Intestine Small	intestine
6	chr11:8891400-8893000	Active TSS	Fetal Muscle Trunk	muscle
7	chr11:8891400-8893200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr11:8891400-8893200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:8891400-8893200	Active TSS	Brain Anterior Caudate	brain
10	chr11:8891400-8893200	Active TSS	Colon Smooth Muscle	Colon
11	chr11:8891400-8893200	Active TSS	Duodenum Mucosa	Duodenum
12	chr11:8891400-8893200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr11:8891400-8893400	Active TSS	Ovary	ovary
14	chr11:8891400-8894000	Active TSS	Stomach Smooth Muscle	stomach
15	chr11:8891600-8892400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
16	chr11:8891600-8893000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:8891600-8893200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:8891600-8893200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:8891600-8893200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr11:8891600-8893200	Bivalent/Poised TSS	Fetal Thymus	thymus
21	chr11:8891600-8893200	Active TSS	Rectal Smooth Muscle	rectum
22	chr11:8891600-8893400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr11:8891600-8893400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:8891600-8893400	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr11:8891600-8893400	Active TSS	Right Atrium	heart
26	chr11:8891600-8893400	Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr11:8891600-8893600	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr11:8891800-8892400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:8891800-8892400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr11:8891800-8892400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
31	chr11:8891800-8892400	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr11:8891800-8892400	Flanking Active TSS	Liver	Liver
33	chr11:8891800-8892600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr11:8891800-8892800	Active TSS	Lung	lung
35	chr11:8891800-8892800	Flanking Bivalent TSS/Enh	Dnd41	blood
36	chr11:8891800-8893000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:8891800-8893000	Active TSS	Fetal Muscle Leg	muscle
38	chr11:8891800-8893200	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr11:8891800-8893200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:8891800-8893200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:8891800-8893200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:8891800-8893200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:8891800-8893200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:8891800-8893200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:8891800-8893200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:8891800-8893200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:8891800-8893200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:8891800-8893200	Active TSS	Aorta	Aorta
49	chr11:8891800-8893200	Active TSS	Brain Angular Gyrus	brain
50	chr11:8891800-8893200	Active TSS	Colonic Mucosa	Colon

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