Variant report

Variant	rs11042104
Chromosome Location	chr11:8890924-8890925
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8701293..8704221-chr11:8890079..8892942,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10743091	0.84[EUR][1000 genomes]
rs10840135	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840137	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042097	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11042098	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11042106	0.89[LWK][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.90[YRI][hapmap]
rs11042115	0.95[YRI][hapmap]
rs11042116	0.94[YRI][hapmap]
rs11042118	0.94[YRI][hapmap]
rs11042148	0.90[MEX][hapmap]
rs1123936	0.83[JPT][hapmap]
rs12049908	0.90[YRI][hapmap]
rs12798322	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1368017	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1529641	0.82[JPT][hapmap]
rs16906256	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980428	0.83[JPT][hapmap]
rs2292049	0.90[CEU][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2568025	0.84[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2568031	0.95[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs2568032	0.95[CHB][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs2568043	0.82[JPT][hapmap]
rs2568045	0.83[JPT][hapmap]
rs2568061	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2568065	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2568092	0.80[MEX][hapmap]
rs2653569	0.81[MEX][hapmap]
rs2742536	0.95[JPT][hapmap]
rs2742537	0.95[JPT][hapmap]
rs2742540	0.89[CHD][hapmap];0.95[JPT][hapmap]
rs2742545	0.95[JPT][hapmap]
rs2742552	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs34874636	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3763913	0.80[MEX][hapmap]
rs3815991	0.90[MEX][hapmap]
rs59025804	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61876202	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7123429	0.95[JPT][hapmap]
rs7127479	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7948452	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11042104	TMEM9B-AS1	cis	Esophagus Muscularis	GTEx
rs11042104	DNHD1	cis	parietal	SCAN
rs11042104	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs11042104	MMP26	cis	cerebellum	SCAN
rs11042104	TMEM9B-AS1	cis	lung	GTEx
rs11042104	TMEM9B-AS1	cis	Thyroid	GTEx
rs11042104	TMEM9B	cis	multi-tissue	Pritchard
rs11042104	CYB5R2	cis	parietal	SCAN
rs11042104	TMEM9B-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11042104	DNHD1	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8878200-8891800	Weak transcription	Psoas Muscle	Psoas
2	chr11:8880200-8892000	Weak transcription	Gastric	stomach
3	chr11:8884400-8891800	Weak transcription	Left Ventricle	heart
4	chr11:8885600-8891400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:8885600-8891400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:8885800-8891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:8885800-8891400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:8885800-8891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:8885800-8891800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr11:8887200-8891400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:8887200-8891600	Weak transcription	Adipose Nuclei	Adipose
12	chr11:8887200-8891800	Weak transcription	Brain Substantia Nigra	brain
13	chr11:8887200-8892000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:8887400-8891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:8888000-8891600	Enhancers	Placenta	Placenta
16	chr11:8888000-8891600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr11:8888200-8891400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr11:8888200-8891400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:8888200-8891600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:8888400-8891400	Enhancers	Fetal Stomach	stomach
21	chr11:8888400-8891800	Weak transcription	Brain Angular Gyrus	brain
22	chr11:8888600-8891400	Enhancers	Fetal Muscle Leg	muscle
23	chr11:8888600-8891800	Weak transcription	Stomach Mucosa	stomach
24	chr11:8888800-8891400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:8888800-8891600	Weak transcription	Right Atrium	heart
26	chr11:8888800-8891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:8888800-8891800	Weak transcription	Colonic Mucosa	Colon
28	chr11:8889000-8891600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr11:8889000-8891600	Weak transcription	HUVEC	blood vessel
30	chr11:8889400-8891400	Enhancers	Fetal Kidney	kidney
31	chr11:8889600-8891000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:8889600-8891200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:8889800-8891200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr11:8889800-8891400	Weak transcription	Fetal Intestine Large	intestine
35	chr11:8889800-8891400	Weak transcription	Fetal Intestine Small	intestine
36	chr11:8889800-8891800	Weak transcription	Lung	lung
37	chr11:8889800-8892000	Weak transcription	Small Intestine	intestine
38	chr11:8890000-8891000	Weak transcription	Ovary	ovary
39	chr11:8890000-8891200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:8890000-8891600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:8890200-8891200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:8890200-8891400	Weak transcription	Fetal Heart	heart
43	chr11:8890200-8891400	Weak transcription	Fetal Lung	lung
44	chr11:8890200-8891400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:8890200-8891400	Weak transcription	A549	lung
46	chr11:8890200-8891400	Enhancers	Osteobl	bone
47	chr11:8890200-8891600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:8890200-8891600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:8890200-8891600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:8890200-8891600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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