Variant report

Variant	rs2657125
Chromosome Location	chr15:58993401-58993402
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	chr15:58990755..58993550-chr15:58994892..58997699,2	K562	blood:

Variant related genes	Relation type
ENSG00000199730	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11071398	0.95[YRI][hapmap]
rs11638244	0.94[YRI][hapmap]
rs11854073	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12439457	0.85[AFR][1000 genomes]
rs12899638	1.00[YRI][hapmap]
rs1427282	1.00[YRI][hapmap]
rs1648532	0.88[YRI][hapmap]
rs2555356	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs28864995	1.00[YRI][hapmap]
rs347115	0.95[YRI][hapmap]
rs347117	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs383902	0.95[YRI][hapmap]
rs387812	0.95[YRI][hapmap]
rs442495	1.00[YRI][hapmap]
rs474875	0.95[YRI][hapmap]
rs4775087	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs56379250	0.82[ASN][1000 genomes]
rs610877	0.95[YRI][hapmap]
rs6494029	1.00[YRI][hapmap]
rs714696	1.00[YRI][hapmap]
rs7161889	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7163162	0.85[AFR][1000 genomes]
rs972801	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2657125	LCOR	cis	Brain Pons	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-58996400	Weak transcription	NHLF	lung
2	chr15:58977200-58998200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:58977200-59004400	Weak transcription	Ovary	ovary
4	chr15:58977200-59007800	Weak transcription	HepG2	liver
5	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:58982600-59008000	Weak transcription	Fetal Brain Male	brain
8	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
9	chr15:58985200-59005000	Weak transcription	HSMMtube	muscle
10	chr15:58985600-58995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:58987400-58993600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:58987400-59012000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:58987600-58995800	Weak transcription	Hela-S3	cervix
15	chr15:58987600-59005000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:58987600-59007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:58989000-58997200	ZNF genes & repeats	GM12878-XiMat	blood
18	chr15:58989400-58996000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:58989800-58994200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:58990000-58994000	Weak transcription	Psoas Muscle	Psoas
22	chr15:58990000-58994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr15:58990000-58996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:58990000-58996000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:58990000-58996200	Weak transcription	Right Atrium	heart
26	chr15:58990000-58997600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr15:58990000-58998400	Weak transcription	Gastric	stomach
28	chr15:58990000-58998400	Weak transcription	Right Ventricle	heart
29	chr15:58990000-58998800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:58990000-59004800	Weak transcription	Pancreas	Pancrea
31	chr15:58990000-59005000	Weak transcription	Spleen	Spleen
32	chr15:58990000-59005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:58990200-58993600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:58990200-58993600	Enhancers	Dnd41	blood
36	chr15:58990200-58993800	Weak transcription	Stomach Mucosa	stomach
37	chr15:58990200-58994400	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr15:58990200-58995800	Weak transcription	Left Ventricle	heart
39	chr15:58990200-58996000	Weak transcription	Lung	lung
40	chr15:58990800-58994600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:58990800-58995800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:58991000-58994600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:58991400-58996400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:58991600-58993600	Weak transcription	Adipose Nuclei	Adipose
45	chr15:58991600-58993600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:58991600-58994000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:58991600-58996800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:58991600-59005200	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:58991800-58993600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:58991800-59005000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links