Variant report

Variant	rs2290549
Chromosome Location	chr3:142742285-142742286
allele	C/T
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	POLR2A	chr3:142741646-142742710	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142736107..142739008-chr3:142740597..142742983,2	K562	blood:
2	chr3:142718039..142721336-chr3:142740977..142744242,3	K562	blood:

Variant related genes	Relation type
U2SURP	TF binding region
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10413	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043898	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10451867	0.85[EUR][1000 genomes]
rs10513184	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs1053950	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10935474	0.82[EUR][1000 genomes]
rs10935475	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935479	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11709036	0.85[CEU][hapmap];0.80[CHB][hapmap]
rs11915462	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11922201	0.88[EUR][1000 genomes]
rs12485790	0.86[EUR][1000 genomes]
rs12490776	0.85[EUR][1000 genomes]
rs12492904	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12695770	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075955	0.85[EUR][1000 genomes]
rs13094293	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1349262	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13715	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs1375814	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1449868	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1449869	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530753	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1532588	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545597	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17557029	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1814565	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs1827159	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839406	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868569	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1868570	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965343	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045306	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124541	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124542	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2124543	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2137586	0.85[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs2175739	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs2353408	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2353409	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353411	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs251490	0.82[CEU][hapmap]
rs251491	0.82[CEU][hapmap]
rs36285	0.82[CEU][hapmap]
rs3821645	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3856697	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3902877	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4030582	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683444	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683721	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683722	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683723	0.85[EUR][1000 genomes]
rs4683724	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56382522	0.90[EUR][1000 genomes]
rs6440129	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440131	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440132	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440133	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440134	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770102	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778454	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781080	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6781887	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783145	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784200	0.89[CEU][hapmap];0.90[CHB][hapmap]
rs6802376	0.81[EUR][1000 genomes]
rs6805417	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806551	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808689	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611721	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623532	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7644475	0.86[EUR][1000 genomes]
rs7648143	0.89[CEU][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649225	0.84[EUR][1000 genomes]
rs7652745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs766360	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs894177	1.00[YRI][hapmap]
rs936194	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936196	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936197	0.85[EUR][1000 genomes]
rs937498	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9814656	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816317	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835348	0.89[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9847059	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9851353	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9862433	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877128	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9877135	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290549	U2SURP	cis	lymphoblastoid	seeQTL
rs2290549	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:142722000-142742400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:142722200-142743000	Weak transcription	Brain Substantia Nigra	brain
4	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:142728000-142742400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:142728400-142748400	Weak transcription	Spleen	Spleen
7	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
8	chr3:142729200-142758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:142729200-142765000	Strong transcription	Dnd41	blood
10	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
11	chr3:142729400-142764800	Strong transcription	K562	blood
12	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:142730200-142743800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:142730200-142753400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
18	chr3:142730400-142754200	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr3:142730600-142753800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:142730800-142758800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:142731000-142744400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:142731000-142749400	Strong transcription	Adipose Nuclei	Adipose
23	chr3:142731000-142754000	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:142731200-142753800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:142732600-142754200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:142732800-142743800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:142732800-142759000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:142732800-142765000	Strong transcription	HSMM	muscle
29	chr3:142733000-142743800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:142733000-142755000	Weak transcription	Stomach Mucosa	stomach
31	chr3:142733200-142744200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:142733200-142754200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:142733400-142750400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:142734000-142758800	Strong transcription	Liver	Liver
36	chr3:142734400-142747800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:142734400-142759000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
39	chr3:142734600-142748400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:142734600-142758800	Strong transcription	GM12878-XiMat	blood
41	chr3:142734800-142743000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:142734800-142756400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:142735000-142745000	Strong transcription	Primary B cells from cord blood	blood
44	chr3:142735000-142749000	Strong transcription	HMEC	breast
45	chr3:142735000-142750800	Strong transcription	A549	lung
46	chr3:142735000-142758800	Strong transcription	Placenta	Placenta
47	chr3:142735200-142742800	Strong transcription	Brain Anterior Caudate	brain
48	chr3:142735200-142744400	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:142735200-142750600	Strong transcription	Fetal Lung	lung
50	chr3:142735200-142753400	Strong transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links