Variant report

Variant	rs2593252
Chromosome Location	chr15:57449165-57449166
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10467927	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10467928	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10467929	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11071308	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11853810	0.90[JPT][hapmap]
rs11856210	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11856411	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12101455	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12591430	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13379847	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1430820	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1430822	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs16977243	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16977270	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16977278	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs17415731	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1841695	0.83[ASN][1000 genomes]
rs1841697	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169467	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2414493	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2593211	0.82[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2593249	0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2593250	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2615227	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs2703614	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733323	0.89[JPT][hapmap]
rs2733333	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2733334	0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs28372003	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28712697	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28781690	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3803453	0.89[JPT][hapmap]
rs58479554	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493900	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67077316	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7162194	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7163267	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7164298	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7169508	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7171073	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7171304	0.90[CEU][hapmap]
rs7173748	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7176873	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7178833	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7180558	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs720290	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs8023736	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8024901	0.89[JPT][hapmap]
rs8026702	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs8031640	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs8032615	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs8034066	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs8034502	0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8034843	0.84[JPT][hapmap]
rs8035916	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8037956	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs8039176	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs8039899	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9302200	0.92[CEU][hapmap];0.82[CHB][hapmap]
rs9806170	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9806199	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs997683	0.90[JPT][hapmap]

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
rs2593252	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs2593252	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57439000-57463400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:57439400-57456000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:57440800-57450400	Weak transcription	Aorta	Aorta
5	chr15:57441200-57450800	Weak transcription	Esophagus	oesophagus
6	chr15:57442400-57450400	Weak transcription	Ovary	ovary
7	chr15:57442600-57450600	Weak transcription	Gastric	stomach
8	chr15:57444200-57456600	Strong transcription	Fetal Thymus	thymus
9	chr15:57444400-57449800	Weak transcription	Left Ventricle	heart
10	chr15:57444400-57450400	Weak transcription	Thymus	Thymus
11	chr15:57444400-57450800	Weak transcription	Fetal Stomach	stomach
12	chr15:57444400-57459000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:57444400-57459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:57444400-57485600	Weak transcription	Placenta	Placenta
15	chr15:57444400-57507400	Weak transcription	K562	blood
16	chr15:57444600-57450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:57444600-57450600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:57444600-57450600	Weak transcription	NH-A	brain
19	chr15:57444600-57451400	Weak transcription	Fetal Intestine Small	intestine
20	chr15:57444600-57452800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:57444600-57455600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:57444600-57458000	Weak transcription	Dnd41	blood
23	chr15:57444600-57458400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:57444600-57459000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:57444600-57459600	Weak transcription	Liver	Liver
26	chr15:57444600-57490200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr15:57444800-57450400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:57444800-57458600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:57444800-57458800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:57444800-57458800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:57444800-57484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:57444800-57484200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:57445000-57450800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:57445000-57455600	Weak transcription	Primary T cells from cord blood	blood
35	chr15:57445000-57461600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:57445200-57450600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:57445200-57452400	Weak transcription	Fetal Intestine Large	intestine
38	chr15:57445200-57466000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:57445400-57458800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:57445400-57478400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:57445600-57450200	Weak transcription	A549	lung
42	chr15:57445600-57450600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:57445600-57450600	Weak transcription	Small Intestine	intestine
44	chr15:57445600-57450800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:57445600-57455800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:57445600-57458800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:57445600-57459000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:57445600-57461400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:57445800-57450600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:57445800-57450600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links