Variant report

Variant	rs28533433
Chromosome Location	chr15:57354261-57354262
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57352117..57354489-chr15:57357081..57359694,2	K562	blood:
2	chr15:57352117..57354569-chr15:57356374..57360031,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10467927	0.81[EUR][1000 genomes]
rs11071303	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856411	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12101455	0.81[EUR][1000 genomes]
rs1430820	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1430822	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16977222	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16977243	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2435907	0.80[AFR][1000 genomes]
rs2439918	0.85[AFR][1000 genomes]
rs2464429	0.83[AFR][1000 genomes]
rs2464430	0.84[AFR][1000 genomes]
rs2470082	0.84[AFR][1000 genomes]
rs2703576	0.86[AFR][1000 genomes]
rs2733177	0.85[AFR][1000 genomes]
rs2733185	0.81[AFR][1000 genomes]
rs28360967	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28372003	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28422021	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28505122	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28541606	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28612876	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28648577	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28649108	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28654848	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28677775	0.85[EUR][1000 genomes]
rs28712697	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28756149	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28814080	0.83[EUR][1000 genomes]
rs28856894	0.80[EUR][1000 genomes]
rs2920265	0.84[AFR][1000 genomes]
rs2920267	0.85[AFR][1000 genomes]
rs2951895	0.86[AFR][1000 genomes]
rs2951903	0.82[AFR][1000 genomes]
rs2951904	0.80[AFR][1000 genomes]
rs2951906	0.82[AFR][1000 genomes]
rs2962991	0.83[AFR][1000 genomes]
rs2962992	0.85[AFR][1000 genomes]
rs58479554	0.81[EUR][1000 genomes]
rs6493900	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67077316	0.81[EUR][1000 genomes]
rs7162194	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7163267	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7164655	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7169053	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169508	0.80[EUR][1000 genomes]
rs7171073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171304	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178833	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8023736	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8023816	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8031516	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8031640	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8032615	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033010	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8034066	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8039899	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8040708	0.86[EUR][1000 genomes]
rs9302200	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9806170	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9806199	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	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	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
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28533433	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs28533433	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
2	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
3	chr15:57328600-57355000	Weak transcription	Dnd41	blood
4	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr15:57336600-57371800	Weak transcription	K562	blood
6	chr15:57339600-57355600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:57339800-57361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
10	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
11	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:57346600-57355000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
14	chr15:57347200-57356200	Weak transcription	Fetal Kidney	kidney
15	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
17	chr15:57348200-57361800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:57348600-57356800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr15:57348800-57355000	Enhancers	Osteobl	bone
20	chr15:57349000-57354400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:57349200-57355400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:57349200-57356600	Enhancers	Brain Substantia Nigra	brain
23	chr15:57349600-57359800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:57349800-57357800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:57349800-57363800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
27	chr15:57350000-57355000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:57350200-57360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:57350200-57363800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:57350400-57355200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:57350400-57356000	Enhancers	HUVEC	blood vessel
32	chr15:57350400-57362400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
34	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr15:57350400-57374000	Weak transcription	Ovary	ovary
36	chr15:57350600-57355400	Enhancers	NHEK	skin
37	chr15:57350800-57356200	Weak transcription	Fetal Heart	heart
38	chr15:57351000-57354600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:57351000-57354600	Enhancers	NH-A	brain
40	chr15:57351000-57356400	Enhancers	HMEC	breast
41	chr15:57351200-57356800	Enhancers	Brain Cingulate Gyrus	brain
42	chr15:57351400-57356400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:57351600-57361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:57351800-57355600	Weak transcription	Thymus	Thymus
45	chr15:57351800-57355800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:57351800-57355800	Weak transcription	Liver	Liver
47	chr15:57351800-57359000	Weak transcription	GM12878-XiMat	blood
48	chr15:57351800-57360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:57351800-57361600	Weak transcription	Primary T cells from cord blood	blood
50	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links