Variant report

Variant	rs28722480
Chromosome Location	chr4:99582072-99582073
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	chr4:99181647..99184072-chr4:99579310..99582613,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAP1GDS1-3	chr4:99581949-99582077	XLOC_003615
2	lnc-RAP1GDS1-3	chr4:99580983-99582077	XLOC_003615
3	lnc-RAP1GDS1-3	chr4:99580055-99585701	ENSG00000260641.1
4	lnc-RAP1GDS1-3	chr4:99580055-99585702	NONHSAT097492

Variant related genes	Relation type
ENSG00000138698	Chromatin interaction
ENSG00000214559	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10022548	0.83[AMR][1000 genomes]
rs28574900	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28591094	0.80[AMR][1000 genomes]
rs28732372	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59383241	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6532756	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9991354	0.85[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28722480	RP11-1299A16.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99580400-99582600	Weak transcription	Small Intestine	intestine
2	chr4:99580400-99583800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:99580400-99584000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr4:99580600-99583400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:99580600-99583800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:99580600-99583800	Weak transcription	Thymus	Thymus
7	chr4:99580600-99584000	Weak transcription	Spleen	Spleen
8	chr4:99580600-99584400	Weak transcription	Adipose Nuclei	Adipose
9	chr4:99580600-99585200	Enhancers	Fetal Lung	lung
10	chr4:99580800-99582200	Enhancers	Fetal Intestine Small	intestine
11	chr4:99580800-99582200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:99580800-99582200	Enhancers	HUVEC	blood vessel
13	chr4:99580800-99583200	Enhancers	Fetal Intestine Large	intestine
14	chr4:99580800-99583800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:99580800-99583800	Enhancers	Primary T cells from cord blood	blood
16	chr4:99580800-99583800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:99580800-99583800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:99580800-99584000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:99580800-99584000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:99580800-99584000	Weak transcription	Lung	lung
21	chr4:99580800-99584200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:99580800-99585200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:99581000-99582200	Weak transcription	Fetal Brain Female	brain
24	chr4:99581000-99583000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:99581000-99583600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:99581000-99584000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:99581000-99585800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:99581200-99582800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:99581200-99584000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr4:99581200-99584000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:99581200-99584000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:99581200-99584000	Weak transcription	Gastric	stomach
33	chr4:99581200-99584200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:99581200-99584200	Weak transcription	Brain Hippocampus Middle	brain
35	chr4:99581200-99584200	Weak transcription	Fetal Muscle Leg	muscle
36	chr4:99581200-99584600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:99581400-99582200	Enhancers	Fetal Heart	heart
38	chr4:99581400-99582200	Enhancers	Stomach Smooth Muscle	stomach
39	chr4:99581400-99582600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr4:99581400-99582600	Enhancers	NHEK	skin
41	chr4:99581400-99582800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr4:99581400-99582800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:99581400-99583000	Enhancers	NHLF	lung
44	chr4:99581400-99583200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:99581400-99583400	Weak transcription	Fetal Thymus	thymus
46	chr4:99581400-99583600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr4:99581400-99583800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:99581400-99583800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:99581400-99584000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:99581400-99584000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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