Variant report

Variant	rs16907241
Chromosome Location	chr11:9926771-9926772
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	chr11:9926719..9929001-chr11:10324531..10327507,2	MCF-7	breast:
2	chr11:9918384..9921801-chr11:9925480..9929741,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254554	Chromatin interaction
ENSG00000148926	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10500710	0.85[JPT][hapmap]
rs10500711	0.85[JPT][hapmap];0.86[YRI][hapmap]
rs10500713	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576435	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1546543	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs16907215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16907238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907257	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171493	0.85[JPT][hapmap]
rs1996062	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs360162	0.85[JPT][hapmap];0.87[YRI][hapmap]
rs360163	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs360166	0.85[JPT][hapmap]
rs360169	0.85[JPT][hapmap]
rs4463836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4542406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59550065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60517573	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938163	0.89[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
2	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
4	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
6	chr11:9913600-9928800	Weak transcription	Right Ventricle	heart
7	chr11:9913800-9927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:9914200-9926800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:9914400-9927600	Weak transcription	Brain Anterior Caudate	brain
10	chr11:9915000-9937200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:9915400-9926800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr11:9915400-9927600	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:9916600-9932600	Weak transcription	Fetal Intestine Small	intestine
14	chr11:9916800-9944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:9916800-9944400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:9917000-9927600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:9917000-9937200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:9917200-9927400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:9917400-9928000	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:9917600-9927200	Weak transcription	Fetal Intestine Large	intestine
21	chr11:9917600-9927600	Weak transcription	Fetal Lung	lung
22	chr11:9917600-9928200	Weak transcription	Liver	Liver
23	chr11:9917600-9928200	Weak transcription	Fetal Heart	heart
24	chr11:9917600-9933200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:9917600-9934200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:9917600-9951800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:9917600-9952400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr11:9917800-9927400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:9917800-9927400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr11:9917800-9927600	Weak transcription	Adipose Nuclei	Adipose
31	chr11:9917800-9933200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:9917800-9952600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:9920000-9933200	Weak transcription	Fetal Stomach	stomach
34	chr11:9921400-9934400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr11:9923200-9926800	Weak transcription	Hela-S3	cervix
36	chr11:9923400-9943600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:9923400-9952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:9924000-9927800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:9924000-9944400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:9924200-9927000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr11:9924400-9927200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:9925000-9927600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr11:9925200-9930000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:9925200-9944400	Weak transcription	Ovary	ovary
45	chr11:9925400-9928800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:9925400-9929600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr11:9925400-9951000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr11:9925400-9952200	Weak transcription	Lung	lung
49	chr11:9925800-9927600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr11:9926000-9927800	Enhancers	NHDF-Ad	bronchial

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