Variant report

Variant	rs11030223
Chromosome Location	chr11:28162284-28162285
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	chr11:28129834..28131357-chr11:28160619..28162492,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169519	Chromatin interaction
ENSG00000121621	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1032090	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1032091	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10767697	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10767705	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767710	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767712	0.81[ASN][1000 genomes]
rs10835259	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10835275	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835280	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835282	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835286	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10835294	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835296	0.90[EUR][1000 genomes]
rs10835298	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835307	0.81[ASN][1000 genomes]
rs10835310	0.84[ASN][1000 genomes]
rs11030193	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11030197	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11030201	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030203	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030204	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030227	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11030228	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11030259	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11030262	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030267	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12294035	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12360577	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12361167	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12806548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1384904	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483861	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564745	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1608871	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17244296	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2046372	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2128956	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2128958	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140886	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2140887	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2354426	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4512801	0.81[ASN][1000 genomes]
rs4923522	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923525	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6484352	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6484357	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6484361	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6484366	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7102481	0.81[ASN][1000 genomes]
rs7105075	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7107992	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7108140	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7117221	0.81[ASN][1000 genomes]
rs7121923	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7127104	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128488	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129953	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7482650	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7924896	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7932126	0.84[ASN][1000 genomes]
rs7944852	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs960357	0.93[EUR][1000 genomes]
rs997555	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9988877	0.84[AMR][1000 genomes];0.84[EUR][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	nsv897150	chr11:28110210-28302792	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1040043	chr11:28118451-28170684	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv897151	chr11:28130191-28208464	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv897152	chr11:28130191-28218303	Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3429359	chr11:28155425-28172758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:28154800-28162600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:28154800-28163000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
3	chr11:28155000-28162800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:28155000-28162800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr11:28155000-28163000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:28156000-28163000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr11:28158800-28162800	ZNF genes & repeats	Dnd41	blood
8	chr11:28159400-28163000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr11:28159600-28162800	ZNF genes & repeats	NHEK	skin
10	chr11:28159800-28162800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr11:28159800-28162800	ZNF genes & repeats	HMEC	breast
12	chr11:28159800-28163000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:28159800-28163000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr11:28159800-28163000	ZNF genes & repeats	Fetal Lung	lung
15	chr11:28159800-28163200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:28160000-28162800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
17	chr11:28160000-28162800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr11:28160200-28162600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:28160200-28162600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:28160200-28162600	ZNF genes & repeats	Ovary	ovary
21	chr11:28160200-28162600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
22	chr11:28160200-28162800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:28160200-28162800	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr11:28160200-28162800	Strong transcription	A549	lung
25	chr11:28160400-28162400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
26	chr11:28160400-28162800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:28160400-28163000	ZNF genes & repeats	Fetal Muscle Leg	muscle
28	chr11:28160600-28162800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
29	chr11:28160800-28162400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:28160800-28162600	ZNF genes & repeats	Liver	Liver
31	chr11:28160800-28162800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:28160800-28162800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
33	chr11:28160800-28163000	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
34	chr11:28160800-28163000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:28161000-28162400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:28161000-28162400	ZNF genes & repeats	NHLF	lung
37	chr11:28161000-28162400	ZNF genes & repeats	Osteobl	bone
38	chr11:28161000-28162600	ZNF genes & repeats	Pancreas	Pancrea
39	chr11:28161000-28162600	ZNF genes & repeats	Placenta Amnion	Placenta Amnion
40	chr11:28161000-28162800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:28161200-28162800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr11:28161200-28163000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
43	chr11:28161400-28162400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
44	chr11:28161400-28162600	ZNF genes & repeats	Right Ventricle	heart
45	chr11:28161400-28163000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
46	chr11:28161400-28163000	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr11:28161600-28162600	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:28161600-28163000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:28161800-28163000	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr11:28161800-28163000	ZNF genes & repeats	Brain Hippocampus Middle	brain

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