Variant report

Variant	rs11229876
Chromosome Location	chr11:58972501-58972502
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	chr11:58939016..58941772-chr11:58971563..58975931,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10896948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896951	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896954	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229866	0.87[AFR][1000 genomes]
rs11229871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229878	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229888	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229890	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229891	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229892	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229893	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229894	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229905	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12225328	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12226710	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12275736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12275799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12284698	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951382	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58943600-58975400	Weak transcription	NHEK	skin
2	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
3	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix
5	chr11:58959600-58974600	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr11:58960400-58974800	Weak transcription	Aorta	Aorta
7	chr11:58962800-58975000	Genic enhancers	Primary B cells from peripheral blood	blood
8	chr11:58963400-58973800	Weak transcription	Primary T cells from cord blood	blood
9	chr11:58964200-58976000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:58964400-58977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:58964800-58975600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:58965800-58978000	Weak transcription	Left Ventricle	heart
13	chr11:58966000-58973200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr11:58966200-58972600	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:58966200-58973400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:58966600-58973800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:58966600-58973800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:58966600-58975400	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:58966800-58974600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr11:58967000-58973000	Strong transcription	Fetal Brain Male	brain
21	chr11:58967000-58975000	Strong transcription	Fetal Brain Female	brain
22	chr11:58967200-58973800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:58968000-58973600	Strong transcription	Brain Anterior Caudate	brain
24	chr11:58968000-58975600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:58968400-58974200	Strong transcription	Ovary	ovary
26	chr11:58968400-58975800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:58968600-58972600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:58968600-58973000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:58968800-58973800	Strong transcription	Brain Cingulate Gyrus	brain
30	chr11:58968800-58974400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:58969000-58973600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:58969000-58973800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:58969000-58974200	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:58969000-58974400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:58969000-58974600	Strong transcription	Fetal Intestine Large	intestine
36	chr11:58969200-58973800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:58969200-58974200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:58969200-58974200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:58969200-58974200	Strong transcription	Liver	Liver
40	chr11:58969200-58974400	Strong transcription	Placenta	Placenta
41	chr11:58969200-58974600	Strong transcription	Fetal Kidney	kidney
42	chr11:58969400-58974400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:58969400-58975000	Strong transcription	Fetal Lung	lung
44	chr11:58969400-58975400	Weak transcription	HepG2	liver
45	chr11:58969600-58973400	Strong transcription	Brain Hippocampus Middle	brain
46	chr11:58970200-58973600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr11:58970400-58974000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr11:58971000-58973400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:58971200-58973400	Strong transcription	Brain Substantia Nigra	brain
50	chr11:58971200-58973800	Strong transcription	Colonic Mucosa	Colon

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