Variant report

Variant	rs2254602
Chromosome Location	chr15:45008434-45008435
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	chr15:45002354-45013577	GM18951	blood:	n/a	n/a
2	POLR2A	chr15:45007038-45012397	K562	blood:	n/a	n/a
3	BCLAF1	chr15:45007019-45008449	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:45002280-45010248	GM12891	blood:	n/a	n/a
5	POLR2A	chr15:45005511-45010190	GM12891	blood:	n/a	n/a
6	POLR2A	chr15:45002253-45014109	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:45002255-45010226	GM12891	blood:	n/a	n/a
8	TBL1XR1	chr15:45002321-45008799	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:45002045-45013680	GM18505	blood:	n/a	n/a
10	POLR2A	chr15:45002139-45014682	GM12878	blood:	n/a	n/a
11	POLR2A	chr15:45002322-45013693	GM19193	blood:	n/a	n/a
12	POLR2A	chr15:45006261-45009707	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:45002192-45013674	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:45007723-45009508	K562	blood:	n/a	n/a
15	SMC3	chr15:45008044-45008591	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:45006806-45013794	U87	brain:	n/a	n/a
17	POLR2A	chr15:45007955-45008442	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:45007084-45009562	HepG2	liver:	n/a	n/a
19	POLR2A	chr15:45008240-45008483	K562	blood:	n/a	n/a
20	POLR2A	chr15:45007049-45008978	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr15:45002251-45013700	GM19099	blood:	n/a	n/a
22	POLR2A	chr15:45002180-45010236	GM12892	blood:	n/a	n/a
23	POLR2A	chr15:45002148-45013709	K562	blood:	n/a	n/a
24	POLR2A	chr15:45007064-45008931	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:45002113-45013784	GM12892	blood:	n/a	n/a
26	MTA3	chr15:45002069-45009622	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:45007730-45008441	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:45006810-45013739	U87	brain:	n/a	n/a
29	POLR2A	chr15:45008425-45010266	U87	brain:	n/a	n/a
30	POLR2A	chr15:45002144-45013852	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:45005490-45008502	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr15:45005682-45009729	K562	blood:	n/a	n/a
33	POLR2A	chr15:45005739-45009592	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:45002233-45013625	GM12892	blood:	n/a	n/a
35	MXI1	chr15:45007082-45009472	GM12878	blood:	n/a	n/a
36	STAT5A	chr15:45002074-45008956	GM12878	blood:	n/a	chr15:45003985-45003997 chr15:45003025-45003037 chr15:45003571-45003582 chr15:45004126-45004137 chr15:45002510-45002522 chr15:45003315-45003326 chr15:45004890-45004901 chr15:45003086-45003094 chr15:45003840-45003852 chr15:45005880-45005888
37	POLR2A	chr15:45002259-45014185	GM12878	blood:	n/a	n/a
38	POLR2A	chr15:45007106-45012394	K562	blood:	n/a	n/a
39	POLR2A	chr15:45002263-45010225	GM12891	blood:	n/a	n/a
40	CHD1	chr15:45002069-45008784	GM12878	blood:	n/a	chr15:45004202-45004209
41	POLR2A	chr15:45002196-45013815	GM12892	blood:	n/a	n/a
42	POLR2A	chr15:45002337-45009450	GM15510	blood:	n/a	n/a
43	POLR2A	chr15:45006998-45010142	K562	blood:	n/a	n/a
44	POLR2A	chr15:45002329-45013687	GM18526	blood:	n/a	n/a
45	WRNIP1	chr15:45005738-45009402	GM12878	blood:	n/a	n/a
46	STAT3	chr15:45008160-45008435	MCF10A-Er-Src	breast:	n/a	n/a
47	NFATC1	chr15:45003186-45009388	GM12878	blood:	n/a	chr15:45008863-45008877
48	POLR2A	chr15:45008022-45008480	HepG2	liver:	n/a	n/a
49	POLR2A	chr15:45002595-45008448	IMR90	lung:	n/a	n/a
50	POLR2A	chr15:45002113-45013783	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44955579..44956510-chr15:45007741..45008547,2	K562	blood:
2	chr15:44953703..44956868-chr15:45007445..45011133,5	MCF-7	breast:
3	chr15:45007310..45009648-chr15:45019472..45022079,3	MCF-7	breast:
4	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM69-2	chr15:45008015-45010343	NONHSAT042188

Variant related genes	Relation type
PATL2	TF binding region
ENSG00000229474	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000104133	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1288094	1.00[AMR][1000 genomes]
rs1669834	0.83[LWK][hapmap];1.00[MKK][hapmap]
rs1669854	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1720723	0.83[LWK][hapmap]
rs1901536	0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1901539	1.00[AMR][1000 genomes]
rs2167594	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2167595	0.84[YRI][hapmap]
rs2444005	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs2444007	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2444011	1.00[AMR][1000 genomes]
rs2462044	1.00[AMR][1000 genomes]
rs2468072	1.00[AMR][1000 genomes]
rs2470916	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2556568	1.00[CHB][hapmap]
rs2960207	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3100129	1.00[AMR][1000 genomes]
rs3100130	1.00[AMR][1000 genomes]
rs3100144	1.00[AMR][1000 genomes]
rs3100145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110178	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110179	0.89[AFR][1000 genomes]
rs3110180	1.00[AMR][1000 genomes]
rs3110673	1.00[AMR][1000 genomes]
rs3110674	1.00[AMR][1000 genomes]
rs34359070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34387827	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34708122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4099	1.00[CHB][hapmap]
rs4625702	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923992	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493125	0.84[YRI][hapmap]

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	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2254602	IQCG	trans	lymphoblastoid	seeQTL
rs2254602	METT5D1	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45003200-45011600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:45003800-45010600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr15:45004200-45012400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr15:45004400-45008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:45004400-45009000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:45004400-45009400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
7	chr15:45004400-45009800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
8	chr15:45004600-45020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:45004800-45008800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:45005000-45018400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:45005000-45018600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:45005200-45011400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
13	chr15:45005400-45010200	Weak transcription	Brain Germinal Matrix	brain
14	chr15:45005600-45009200	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:45005800-45009000	Transcr. at gene 5' and 3'	Primary T killer naive cells fromperipheralblood	blood
16	chr15:45005800-45009200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
17	chr15:45006000-45012200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:45006200-45010000	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
19	chr15:45006400-45009200	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:45006600-45008800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
21	chr15:45006600-45011200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:45006600-45011200	Strong transcription	HSMM	muscle
23	chr15:45006800-45008600	Weak transcription	Stomach Mucosa	stomach
24	chr15:45006800-45008800	Genic enhancers	Dnd41	blood
25	chr15:45006800-45009800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
26	chr15:45006800-45012000	Strong transcription	Osteobl	bone
27	chr15:45007000-45009200	Strong transcription	HepG2	liver
28	chr15:45007000-45009800	Weak transcription	Fetal Intestine Small	intestine
29	chr15:45007000-45010600	Strong transcription	K562	blood
30	chr15:45007000-45010800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:45007000-45011200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr15:45007000-45011400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:45007000-45011400	Strong transcription	HUVEC	blood vessel
34	chr15:45007000-45011600	Strong transcription	NH-A	brain
35	chr15:45007200-45008800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
36	chr15:45007200-45009000	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:45007200-45009000	Genic enhancers	Fetal Thymus	thymus
38	chr15:45007200-45009000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
39	chr15:45007200-45009600	Strong transcription	Fetal Intestine Large	intestine
40	chr15:45007200-45009600	Strong transcription	NHEK	skin
41	chr15:45007200-45010800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:45007200-45011200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:45007200-45011200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:45007200-45011400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:45007200-45011600	Genic enhancers	Primary monocytes fromperipheralblood	blood
46	chr15:45007200-45011600	Strong transcription	HSMMtube	muscle
47	chr15:45007200-45012000	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr15:45007400-45008800	Strong transcription	Fetal Stomach	stomach
49	chr15:45007400-45008800	Genic enhancers	Left Ventricle	heart
50	chr15:45007400-45008800	Genic enhancers	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links