Variant report

Variant	rs28649108
Chromosome Location	chr15:57264380-57264381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57210716..57212486-chr15:57263351..57264921,2	K562	blood:
2	chr15:57263359..57266200-chr15:57266241..57268315,2	K562	blood:
3	chr15:57262336..57264742-chr15:57265375..57267744,2	K562	blood:
4	chr15:57253721..57256073-chr15:57262899..57264820,2	K562	blood:
5	chr15:57208964..57210715-chr15:57261991..57264737,2	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11071303	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856411	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12901355	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1430820	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1430822	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16977153	0.85[ASN][1000 genomes]
rs16977222	0.87[AMR][1000 genomes];0.89[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28422021	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28505122	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28533433	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28541606	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28612876	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28654848	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28677775	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28756149	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28814080	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28856894	0.88[EUR][1000 genomes]
rs4774245	0.86[ASN][1000 genomes]
rs4774247	0.82[AFR][1000 genomes]
rs7162194	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164655	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169053	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7171073	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7171304	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176873	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178833	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8023816	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8031516	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031640	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032615	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033010	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8034066	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8035485	0.88[ASN][1000 genomes]
rs8039899	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8040708	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9302200	0.87[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
rs28649108	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs28649108	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57256200-57264400	Weak transcription	NH-A	brain
2	chr15:57256200-57265200	Weak transcription	Fetal Brain Male	brain
3	chr15:57256200-57265800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:57256400-57265200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:57256800-57264400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:57256800-57277200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:57257200-57264600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:57257200-57274600	Weak transcription	Adipose Nuclei	Adipose
9	chr15:57257800-57265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:57259400-57268200	Enhancers	HepG2	liver
11	chr15:57259800-57264600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:57260000-57272200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:57260000-57272400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:57260600-57267000	Enhancers	Dnd41	blood
15	chr15:57261000-57269400	Weak transcription	Psoas Muscle	Psoas
16	chr15:57261200-57264800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:57261200-57272800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:57261200-57279000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:57261400-57264600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:57261400-57265400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:57261400-57272000	Weak transcription	Colon Smooth Muscle	Colon
22	chr15:57261400-57275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:57262000-57264600	Weak transcription	Brain Anterior Caudate	brain
24	chr15:57262000-57269400	Weak transcription	Ovary	ovary
25	chr15:57262000-57269600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:57262200-57264800	Weak transcription	Fetal Lung	lung
27	chr15:57262200-57266000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:57262200-57270800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:57262200-57280000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:57262400-57266000	Weak transcription	Liver	Liver
31	chr15:57263000-57264600	Enhancers	Fetal Intestine Small	intestine
32	chr15:57263000-57264600	Genic enhancers	Fetal Thymus	thymus
33	chr15:57263000-57266200	Enhancers	Small Intestine	intestine
34	chr15:57263200-57266600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr15:57263400-57265000	Enhancers	Stomach Mucosa	stomach
36	chr15:57263400-57266200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:57263400-57266200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:57263400-57266400	Enhancers	K562	blood
39	chr15:57263600-57264600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr15:57263600-57264800	Enhancers	Duodenum Mucosa	Duodenum
41	chr15:57263600-57265000	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr15:57263600-57265000	Enhancers	Brain Angular Gyrus	brain
43	chr15:57263600-57265000	Enhancers	Brain Germinal Matrix	brain
44	chr15:57263600-57265000	Enhancers	Osteobl	bone
45	chr15:57263600-57265800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr15:57263600-57266200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr15:57263600-57266200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:57263600-57266200	Enhancers	Brain Cingulate Gyrus	brain
49	chr15:57263600-57266200	Enhancers	Brain Hippocampus Middle	brain
50	chr15:57263600-57266400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links