Variant report

Variant	rs28488729
Chromosome Location	chr14:55646295-55646296
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55517066..55519736-chr14:55644348..55646551,3	MCF-7	breast:
2	chr14:55645788..55648762-chr14:55649731..55651963,3	K562	blood:
3	chr14:55643693..55646676-chr14:55654219..55656043,3	K562	blood:
4	chr14:55641769..55647288-chr14:55647379..55651271,6	K562	blood:

Variant related genes	Relation type
ENSG00000168175	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10129944	1.00[EUR][1000 genomes]
rs10132251	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10133318	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10133839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10134482	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10134533	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10135042	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10137382	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10138287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10140700	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10141962	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10142150	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10142435	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10143190	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10146432	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10148371	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10149038	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10151981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10438128	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13379284	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17128204	1.00[EUR][1000 genomes]
rs17128286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17128299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17128411	1.00[EUR][1000 genomes]
rs28415601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28458773	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459500	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28584735	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34630492	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60302297	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60342915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9323281	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035158	chr14:55638386-55684228	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3399240	chr14:55646074-55646374	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55598600-55656600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:55605200-55656000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr14:55605400-55657000	Weak transcription	Fetal Kidney	kidney
4	chr14:55606600-55656000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:55607000-55656000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr14:55607200-55652200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr14:55607600-55651800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr14:55607600-55655200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:55610600-55651600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr14:55610600-55655400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr14:55610600-55655600	Strong transcription	Dnd41	blood
12	chr14:55610800-55656000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr14:55611000-55656000	Weak transcription	Fetal Heart	heart
14	chr14:55611600-55656600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:55613400-55657800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:55619200-55646800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr14:55619800-55647400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr14:55622600-55649000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr14:55623600-55657000	Weak transcription	Fetal Muscle Leg	muscle
20	chr14:55629000-55650400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr14:55629200-55655600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr14:55629400-55650600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr14:55629400-55652000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr14:55630200-55656600	Weak transcription	Fetal Brain Female	brain
25	chr14:55631200-55649400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr14:55631200-55650400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:55632400-55656200	Weak transcription	HSMM	muscle
28	chr14:55632600-55646800	Weak transcription	Osteobl	bone
29	chr14:55632600-55647000	Weak transcription	NHLF	lung
30	chr14:55634200-55655400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr14:55634400-55656200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr14:55635000-55647200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr14:55635400-55646800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr14:55637200-55655600	Strong transcription	Fetal Thymus	thymus
35	chr14:55637800-55649600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr14:55638200-55648800	Weak transcription	Fetal Lung	lung
37	chr14:55638200-55656200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr14:55638600-55657200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr14:55638800-55646400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr14:55639800-55654200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr14:55641600-55648800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr14:55641600-55649000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr14:55641800-55646600	Strong transcription	GM12878-XiMat	blood
44	chr14:55642600-55647800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:55642600-55649400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr14:55643600-55647800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr14:55643800-55646600	Strong transcription	NH-A	brain
48	chr14:55643800-55652000	Strong transcription	A549	lung
49	chr14:55644200-55646600	Weak transcription	HUVEC	blood vessel
50	chr14:55644400-55648400	Strong transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links