Variant report

Variant	rs28677775
Chromosome Location	chr15:57261714-57261715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:57261481-57261797	MCF-7	breast:	n/a	n/a
2	ZNF217	chr15:57261558-57261949	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57210057..57212896-chr15:57260738..57263139,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222586	TF binding region
ENSG00000137871	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11071303	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856411	0.84[EUR][1000 genomes]
rs12901355	0.81[EUR][1000 genomes]
rs1430820	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1430822	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16977153	0.86[ASN][1000 genomes]
rs16977222	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17415731	0.97[ASN][1000 genomes]
rs1820994	0.84[ASN][1000 genomes]
rs28360967	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28422021	0.84[EUR][1000 genomes]
rs28505122	0.87[EUR][1000 genomes]
rs28533433	0.85[EUR][1000 genomes]
rs28541606	0.84[EUR][1000 genomes]
rs28612876	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28616268	0.81[EUR][1000 genomes]
rs28648577	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28649108	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28654848	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28756149	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28814080	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28856894	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4774245	0.88[ASN][1000 genomes]
rs4774247	0.82[AFR][1000 genomes]
rs67149912	0.80[EUR][1000 genomes]
rs7162194	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164655	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169053	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7171073	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7171304	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176873	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178833	0.89[ASN][1000 genomes]
rs8023816	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8031516	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031640	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8032615	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8033010	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8034066	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8035485	0.89[ASN][1000 genomes]
rs8039899	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040708	0.91[EUR][1000 genomes]
rs9302200	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28677775	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs28677775	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256200-57263400	Weak transcription	Lung	lung
2	chr15:57256200-57264400	Weak transcription	NH-A	brain
3	chr15:57256200-57265200	Weak transcription	Fetal Brain Male	brain
4	chr15:57256200-57265800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:57256400-57263600	Weak transcription	Brain Germinal Matrix	brain
6	chr15:57256400-57264000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:57256400-57265200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr15:57256800-57263000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr15:57256800-57263600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:57256800-57263600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:57256800-57264400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:57257200-57264600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
15	chr15:57257400-57263600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:57257800-57265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr15:57258000-57263600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:57258200-57264000	Weak transcription	NHDF-Ad	bronchial
19	chr15:57259400-57261800	Enhancers	Primary T cells from cord blood	blood
20	chr15:57259400-57262000	Enhancers	Brain Substantia Nigra	brain
21	chr15:57259400-57262200	Enhancers	Brain Hippocampus Middle	brain
22	chr15:57259400-57262400	Enhancers	Liver	Liver
23	chr15:57259400-57262400	Enhancers	A549	lung
24	chr15:57259400-57268200	Enhancers	HepG2	liver
25	chr15:57259600-57262000	Enhancers	Brain Anterior Caudate	brain
26	chr15:57259600-57262200	Enhancers	Thymus	Thymus
27	chr15:57259800-57264600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:57260000-57263800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:57260000-57272200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:57260000-57272400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr15:57260200-57262000	Enhancers	Pancreas	Pancrea
32	chr15:57260200-57263800	Weak transcription	Fetal Heart	heart
33	chr15:57260400-57262200	Enhancers	Small Intestine	intestine
34	chr15:57260600-57262000	Enhancers	Ovary	ovary
35	chr15:57260600-57262200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr15:57260600-57262200	Enhancers	Fetal Intestine Small	intestine
37	chr15:57260600-57262200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr15:57260600-57262600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr15:57260600-57267000	Enhancers	Dnd41	blood
40	chr15:57260800-57262000	Enhancers	Esophagus	oesophagus
41	chr15:57260800-57262000	Enhancers	Fetal Intestine Large	intestine
42	chr15:57261000-57261800	Weak transcription	Spleen	Spleen
43	chr15:57261000-57262000	Genic enhancers	Fetal Thymus	thymus
44	chr15:57261000-57262200	Flanking Active TSS	NHEK	skin
45	chr15:57261000-57263600	Weak transcription	Brain Angular Gyrus	brain
46	chr15:57261000-57263800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:57261000-57269400	Weak transcription	Psoas Muscle	Psoas
48	chr15:57261200-57262000	Weak transcription	Colonic Mucosa	Colon
49	chr15:57261200-57263000	Weak transcription	Right Atrium	heart
50	chr15:57261200-57263200	Weak transcription	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links