Variant report

Variant	rs28468660
Chromosome Location	chr4:151154292-151154293
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	chr4:151151694..151154346-chr4:151156104..151158650,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12374344	0.92[ASN][1000 genomes]
rs13435901	0.86[ASN][1000 genomes]
rs2305980	0.88[ASN][1000 genomes]
rs28405622	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4696597	0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62346572	0.92[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	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28468660	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151130600-151156000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:151138800-151169800	Weak transcription	Spleen	Spleen
3	chr4:151139600-151177400	Weak transcription	Brain Substantia Nigra	brain
4	chr4:151139600-151181000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:151140000-151175000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:151142200-151172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:151146200-151169200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr4:151146400-151157400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:151146400-151157400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:151146400-151165600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:151146600-151156400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr4:151146600-151165600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:151150800-151155000	Weak transcription	Right Ventricle	heart
14	chr4:151150800-151156800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:151150800-151156800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr4:151150800-151157800	Weak transcription	Fetal Kidney	kidney
17	chr4:151150800-151170800	Weak transcription	Pancreas	Pancrea
18	chr4:151151000-151155800	Weak transcription	Fetal Stomach	stomach
19	chr4:151151400-151156600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:151151400-151157200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr4:151151400-151158400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:151151800-151156800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:151151800-151165600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:151152000-151157000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:151152000-151157000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:151152000-151157200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:151152000-151160200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:151152400-151156800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:151152400-151176400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:151152800-151164200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:151153000-151156800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:151153000-151156800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:151153200-151155600	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:151153400-151156000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:151153400-151156400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:151153400-151156400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr4:151153400-151156800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:151153600-151154800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:151153600-151154800	Weak transcription	Fetal Brain Male	brain
40	chr4:151153600-151155200	Strong transcription	HSMM	muscle
41	chr4:151153600-151155200	Strong transcription	HSMMtube	muscle
42	chr4:151153600-151155400	Strong transcription	Osteobl	bone
43	chr4:151153600-151155600	Strong transcription	Ovary	ovary
44	chr4:151153600-151155800	Strong transcription	Colon Smooth Muscle	Colon
45	chr4:151153600-151156200	Strong transcription	Brain Anterior Caudate	brain
46	chr4:151153600-151156400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:151153600-151156400	Strong transcription	Adipose Nuclei	Adipose
48	chr4:151153600-151156400	Strong transcription	Fetal Muscle Leg	muscle
49	chr4:151153600-151156600	Weak transcription	Fetal Lung	lung
50	chr4:151153600-151156600	Strong transcription	Stomach Smooth Muscle	stomach

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