Variant report

Variant	rs2742543
Chromosome Location	chr11:8890569-8890570
allele	A/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:
2	chr11:8854026..8855722-chr11:8888927..8890740,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166444	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10840149	1.00[EUR][1000 genomes]
rs11042155	1.00[EUR][1000 genomes]
rs1989143	1.00[EUR][1000 genomes]
rs2195812	1.00[EUR][1000 genomes]
rs2256067	0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2262323	1.00[EUR][1000 genomes]
rs2436178	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2568021	1.00[EUR][1000 genomes]
rs2568023	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs2568024	1.00[EUR][1000 genomes]
rs2568026	1.00[EUR][1000 genomes]
rs2568027	1.00[EUR][1000 genomes]
rs2568028	0.89[AMR][1000 genomes]
rs2568030	0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2568041	1.00[EUR][1000 genomes]
rs2568055	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2568058	0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2568060	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2568063	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2568072	1.00[EUR][1000 genomes]
rs2568083	1.00[EUR][1000 genomes]
rs2653561	1.00[EUR][1000 genomes]
rs2653563	0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2653571	1.00[EUR][1000 genomes]
rs2653583	1.00[EUR][1000 genomes]
rs2653584	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs2653585	1.00[EUR][1000 genomes]
rs2653600	1.00[EUR][1000 genomes]
rs2653608	1.00[EUR][1000 genomes]
rs2653614	0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2653615	0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2742469	1.00[EUR][1000 genomes]
rs2742479	1.00[EUR][1000 genomes]
rs2742482	1.00[EUR][1000 genomes]
rs2742507	1.00[EUR][1000 genomes]
rs2742508	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs2742518	1.00[EUR][1000 genomes]
rs2742526	1.00[EUR][1000 genomes]
rs2742527	1.00[EUR][1000 genomes]
rs2742539	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2742548	0.81[YRI][hapmap]
rs2742551	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6416158	1.00[EUR][1000 genomes]
rs6416159	1.00[EUR][1000 genomes]
rs7104415	1.00[EUR][1000 genomes]
rs73410028	1.00[EUR][1000 genomes]
rs73410031	1.00[EUR][1000 genomes]
rs73410040	1.00[EUR][1000 genomes]
rs7395934	1.00[EUR][1000 genomes]
rs7396042	1.00[EUR][1000 genomes]
rs7396427	1.00[EUR][1000 genomes]
rs7479998	1.00[EUR][1000 genomes]
rs7932678	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7936297	1.00[EUR][1000 genomes]
rs7950826	1.00[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

No data

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	chr11:8888000-8890600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:8888000-8890800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:8888000-8891600	Enhancers	Placenta	Placenta
18	chr11:8888000-8891600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr11:8888200-8891400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:8888200-8891400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr11:8888200-8891600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:8888400-8890600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:8888400-8891400	Enhancers	Fetal Stomach	stomach
24	chr11:8888400-8891800	Weak transcription	Brain Angular Gyrus	brain
25	chr11:8888600-8891400	Enhancers	Fetal Muscle Leg	muscle
26	chr11:8888600-8891800	Weak transcription	Stomach Mucosa	stomach
27	chr11:8888800-8891400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr11:8888800-8891600	Weak transcription	Right Atrium	heart
29	chr11:8888800-8891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:8888800-8891800	Weak transcription	Colonic Mucosa	Colon
31	chr11:8889000-8891600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr11:8889000-8891600	Weak transcription	HUVEC	blood vessel
33	chr11:8889400-8890600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:8889400-8890800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:8889400-8891400	Enhancers	Fetal Kidney	kidney
36	chr11:8889600-8890800	Flanking Active TSS	NHDF-Ad	bronchial
37	chr11:8889600-8891000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:8889600-8891200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:8889800-8891200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:8889800-8891400	Weak transcription	Fetal Intestine Large	intestine
41	chr11:8889800-8891400	Weak transcription	Fetal Intestine Small	intestine
42	chr11:8889800-8891800	Weak transcription	Lung	lung
43	chr11:8889800-8892000	Weak transcription	Small Intestine	intestine
44	chr11:8890000-8890800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:8890000-8890800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr11:8890000-8891000	Weak transcription	Ovary	ovary
47	chr11:8890000-8891200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:8890000-8891600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:8890200-8891200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:8890200-8891400	Weak transcription	Fetal Heart	heart

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