Variant report

Variant	rs541840
Chromosome Location	chr15:56991849-56991850
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56990532..56992149-chr15:56993959..56995871,2	K562	blood:
2	chr15:56990453..56992167-chr7:33100522..33103358,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122643	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10851611	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12898673	1.00[AMR][1000 genomes]
rs2170460	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2414481	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435894	1.00[AMR][1000 genomes]
rs4143730	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4448877	1.00[AMR][1000 genomes]
rs475512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4774880	1.00[AMR][1000 genomes]
rs4774882	1.00[AMR][1000 genomes]
rs4774883	1.00[AMR][1000 genomes]
rs479060	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs508037	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493878	1.00[AMR][1000 genomes]
rs6493879	1.00[AMR][1000 genomes]
rs6493881	1.00[AMR][1000 genomes]
rs795035	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs795036	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8025919	1.00[AMR][1000 genomes]
rs8043381	1.00[AMR][1000 genomes]
rs989535	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
2	chr15:56928400-56996800	Weak transcription	Gastric	stomach
3	chr15:56937400-57000200	Weak transcription	Colonic Mucosa	Colon
4	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
5	chr15:56959200-56992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:56960800-56992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:56961200-56992200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:56968400-56992000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:56968400-56992000	Weak transcription	HSMMtube	muscle
10	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:56976400-56992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:56978000-56992000	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:56978600-56992000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:56983200-56992800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:56983400-56992600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:56984000-56998800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:56986200-56992800	Weak transcription	Stomach Mucosa	stomach
18	chr15:56987200-56999600	Strong transcription	Fetal Thymus	thymus
19	chr15:56988600-56997200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:56988800-56997200	Strong transcription	Liver	Liver
21	chr15:56988800-57008400	Weak transcription	Fetal Heart	heart
22	chr15:56989200-56992000	Weak transcription	Fetal Kidney	kidney
23	chr15:56989400-56992000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:56989600-56992400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:56989800-56992200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:56989800-56998400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr15:56990000-56992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:56990000-56993400	Strong transcription	NH-A	brain
29	chr15:56990000-56993600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:56990000-56994200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr15:56990000-56998400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:56990000-56999000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:56990000-56999200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:56990200-56993000	Strong transcription	Primary hematopoietic stem cells	blood
35	chr15:56990200-56993200	Strong transcription	Brain Anterior Caudate	brain
36	chr15:56990200-56993200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr15:56990200-56993200	Strong transcription	A549	lung
38	chr15:56990200-56993400	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:56990200-56993400	Strong transcription	Duodenum Mucosa	Duodenum
40	chr15:56990200-56993400	Strong transcription	Placenta	Placenta
41	chr15:56990200-56993400	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:56990200-56994000	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:56990200-56994400	Strong transcription	NHDF-Ad	bronchial
44	chr15:56990200-56995600	Strong transcription	Fetal Lung	lung
45	chr15:56990200-56995800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr15:56990200-56996600	Strong transcription	Dnd41	blood
47	chr15:56990200-56996800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:56990200-56997200	Strong transcription	Primary B cells from cord blood	blood
49	chr15:56990200-56997200	Strong transcription	Osteobl	bone
50	chr15:56990200-56998400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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