Variant report

Variant	rs28654848
Chromosome Location	chr15:57284372-57284373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57281787..57284402-chr15:57285432..57287690,2	K562	blood:
2	chr15:57277206..57280483-chr15:57280538..57284418,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11071303	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856411	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12901355	0.84[EUR][1000 genomes]
rs1430820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430822	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977153	0.85[ASN][1000 genomes]
rs16977222	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17415731	0.97[ASN][1000 genomes]
rs1820994	0.86[ASN][1000 genomes]
rs28360967	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28422021	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28505122	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28533433	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28541606	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28612876	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649108	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28677775	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28756149	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28814080	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28856894	0.88[EUR][1000 genomes]
rs4774245	0.85[ASN][1000 genomes]
rs7162194	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164655	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169053	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171073	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7171304	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7176873	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178833	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8023816	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031516	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031640	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032615	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033010	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034066	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035485	0.88[ASN][1000 genomes]
rs8039899	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040708	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
rs28654848	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs28654848	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57273000-57285800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
4	chr15:57274000-57287600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:57274200-57289200	Weak transcription	Fetal Muscle Leg	muscle
6	chr15:57274200-57295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:57276200-57289200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:57276600-57288000	Weak transcription	Aorta	Aorta
11	chr15:57276800-57288600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:57277000-57285400	Weak transcription	Fetal Intestine Large	intestine
13	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:57277600-57287600	Weak transcription	Brain Germinal Matrix	brain
15	chr15:57277800-57285000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:57278000-57285400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:57278600-57295400	Weak transcription	NH-A	brain
18	chr15:57279400-57300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:57279800-57300200	Weak transcription	Psoas Muscle	Psoas
21	chr15:57280600-57286800	Weak transcription	Fetal Brain Male	brain
22	chr15:57280600-57294000	Weak transcription	HSMMtube	muscle
23	chr15:57281200-57287600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:57281600-57285600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:57282000-57284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:57282000-57285000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:57282000-57285000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:57282000-57285000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:57282000-57285200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:57282000-57285200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:57282000-57285400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:57282000-57285400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:57282000-57285400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:57282000-57285600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:57282000-57289200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:57282000-57289800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:57282000-57295400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr15:57282000-57295400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:57282000-57295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr15:57282200-57285000	Weak transcription	Primary B cells from cord blood	blood
43	chr15:57282200-57285400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:57282200-57285400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:57282200-57285400	Weak transcription	Fetal Lung	lung
46	chr15:57282200-57285400	Weak transcription	HSMM	muscle
47	chr15:57282200-57285600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:57282200-57285600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:57282200-57285600	Weak transcription	A549	lung
50	chr15:57282200-57285600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links