Variant report

Variant	rs2653566
Chromosome Location	chr11:8889818-8889819
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8854026..8855722-chr11:8888927..8890740,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10734638	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11042099	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1811367	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060157	0.88[EUR][1000 genomes]
rs2568029	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2568035	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568056	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568078	0.94[EUR][1000 genomes]
rs2653558	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2653609	0.83[EUR][1000 genomes]
rs2653618	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742483	0.85[EUR][1000 genomes]
rs2742502	0.92[EUR][1000 genomes]
rs2742549	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2742553	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34152382	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34275210	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34371023	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34418236	0.81[EUR][1000 genomes]
rs34581555	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34769330	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35563381	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35580466	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35909878	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36100955	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36180552	0.81[EUR][1000 genomes]
rs4910068	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7117900	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2653566	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8863200-8890400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:8878200-8891800	Weak transcription	Psoas Muscle	Psoas
3	chr11:8880200-8892000	Weak transcription	Gastric	stomach
4	chr11:8884400-8891800	Weak transcription	Left Ventricle	heart
5	chr11:8885600-8891400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:8885600-8891400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:8885800-8891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:8885800-8891400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:8885800-8891400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr11:8885800-8891800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:8887000-8890200	Enhancers	Fetal Lung	lung
12	chr11:8887200-8891400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:8887200-8891600	Weak transcription	Adipose Nuclei	Adipose
14	chr11:8887200-8891800	Weak transcription	Brain Substantia Nigra	brain
15	chr11:8887200-8892000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:8887400-8891400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:8888000-8890200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:8888000-8890400	Enhancers	NH-A	brain
19	chr11:8888000-8890600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:8888000-8890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:8888000-8891600	Enhancers	Placenta	Placenta
22	chr11:8888000-8891600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr11:8888200-8890000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:8888200-8890200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:8888200-8890400	Enhancers	NHEK	skin
26	chr11:8888200-8891400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr11:8888200-8891400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr11:8888200-8891600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr11:8888400-8890600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:8888400-8891400	Enhancers	Fetal Stomach	stomach
31	chr11:8888400-8891800	Weak transcription	Brain Angular Gyrus	brain
32	chr11:8888600-8891400	Enhancers	Fetal Muscle Leg	muscle
33	chr11:8888600-8891800	Weak transcription	Stomach Mucosa	stomach
34	chr11:8888800-8891400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr11:8888800-8891600	Weak transcription	Right Atrium	heart
36	chr11:8888800-8891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr11:8888800-8891800	Weak transcription	Colonic Mucosa	Colon
38	chr11:8889000-8891600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:8889000-8891600	Weak transcription	HUVEC	blood vessel
40	chr11:8889400-8890200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr11:8889400-8890200	Enhancers	HMEC	breast
42	chr11:8889400-8890200	Enhancers	HSMM	muscle
43	chr11:8889400-8890400	Enhancers	Colon Smooth Muscle	Colon
44	chr11:8889400-8890400	Flanking Active TSS	Hela-S3	cervix
45	chr11:8889400-8890600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:8889400-8890800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:8889400-8891400	Enhancers	Fetal Kidney	kidney
48	chr11:8889600-8890000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:8889600-8890000	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr11:8889600-8890000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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