Variant report

Variant	rs2254835
Chromosome Location	chr15:45006618-45006619
allele	A/C
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	chr15:45002280-45010248	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:45005511-45010190	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:45002253-45014109	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:45006436-45006730	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr15:45002255-45010226	GM12891	blood:	n/a	n/a
7	POLR2A	chr15:45005695-45007424	A549	lung:	n/a	n/a
8	TBL1XR1	chr15:45002321-45008799	GM12878	blood:	n/a	n/a
9	POU2F2	chr15:45006501-45006976	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:45002045-45013680	GM18505	blood:	n/a	n/a
11	POLR2A	chr15:45002139-45014682	GM12878	blood:	n/a	n/a
12	BCLAF1	chr15:45005533-45006660	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:45005722-45006696	HL-60	blood:	n/a	n/a
14	POLR2A	chr15:45006260-45007079	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:45002322-45013693	GM19193	blood:	n/a	n/a
16	POLR2A	chr15:45006261-45009707	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr15:45002192-45013674	GM12891	blood:	n/a	n/a
18	POLR2A	chr15:45006225-45006961	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:45005706-45006764	U87	brain:	n/a	n/a
20	POLR2A	chr15:45006351-45006629	MCF10A-Er-Src	breast:	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	chr15:45002801-45006834	U87	brain:	n/a	n/a
24	POLR2A	chr15:45002148-45013709	K562	blood:	n/a	n/a
25	POLR2A	chr15:45003365-45006623	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:45002113-45013784	GM12892	blood:	n/a	n/a
27	MTA3	chr15:45002069-45009622	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:45002773-45008277	U87	brain:	n/a	n/a
29	POLR2A	chr15:45006319-45006625	K562	blood:	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	STAT5A	chr15:45006322-45006744	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:45005739-45009592	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:45002233-45013625	GM12892	blood:	n/a	n/a
36	BCL11A	chr15:45006263-45006631	GM12878	blood:	n/a	n/a
37	MXI1	chr15:45002327-45006676	GM12878	blood:	n/a	n/a
38	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
39	POLR2A	chr15:45002259-45014185	GM12878	blood:	n/a	n/a
40	POLR2A	chr15:45005158-45006729	U87	brain:	n/a	n/a
41	POLR2A	chr15:45002263-45010225	GM12891	blood:	n/a	n/a
42	POU2F2	chr15:45006188-45006731	GM12878	blood:	n/a	chr15:45006383-45006398
43	NFATC1	chr15:45003182-45008371	GM12878	blood:	n/a	n/a
44	CHD1	chr15:45002069-45008784	GM12878	blood:	n/a	chr15:45004202-45004209
45	POLR2A	chr15:45002196-45013815	GM12892	blood:	n/a	n/a
46	POLR2A	chr15:45002337-45009450	GM15510	blood:	n/a	n/a
47	BCLAF1	chr15:45005701-45006753	GM12878	blood:	n/a	n/a
48	RFX5	chr15:45001843-45006625	IMR90	lung:	n/a	chr15:45003663-45003672
49	POLR2A	chr15:45002329-45013687	GM18526	blood:	n/a	n/a
50	WRNIP1	chr15:45005738-45009402	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45004559..45007244-chr15:45019568..45021417,3	MCF-7	breast:
2	chr15:44951739..44957508-chr15:45000588..45008057,33	K562	blood:
3	chr15:44980888..44990623-chr15:45002366..45006726,14	K562	blood:
4	chr15:44952988..44962373-chr15:45002018..45007307,26	MCF-7	breast:
5	chr15:44968819..44972092-chr15:45002551..45007992,5	K562	blood:
6	chr15:44951575..44958275-chr15:45001046..45006983,19	MCF-7	breast:
7	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:

Variant related genes	Relation type
B2M	TF binding region
PATL2	TF binding region
ENSG00000104133	Chromatin interaction
ENSG00000206957	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000229474	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1060392	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1295358	0.85[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs14711	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1901534	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1901537	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs2084835	0.80[MEX][hapmap]
rs2123149	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2254831	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2290331	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2443976	0.84[EUR][1000 genomes]
rs2444003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2444009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2444010	0.85[EUR][1000 genomes]
rs2468064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs2468074	0.86[EUR][1000 genomes]
rs2468075	0.84[EUR][1000 genomes]
rs2468077	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs2470911	0.83[YRI][hapmap]
rs2470914	0.86[EUR][1000 genomes]
rs3100139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3100142	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3110172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3110173	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3110174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3110176	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3110182	0.85[EUR][1000 genomes]
rs3110662	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3110675	0.84[EUR][1000 genomes]
rs6493108	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493109	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[ASN][1000 genomes]
rs7165535	0.80[MEX][hapmap]
rs7172083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935886	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2254835	TRIM69	cis	Adipose Subcutaneous	GTEx
rs2254835	TRIM69	cis	parietal	SCAN
rs2254835	TRIM69	cis	Artery Tibial	GTEx
rs2254835	TRIM69	cis	cerebellum	SCAN
rs2254835	CHST14	cis	parietal	SCAN
rs2254835	TRIM69	cis	Frontal Cortex	GTEx
rs2254835	CHP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45002200-45006800	Active TSS	Colonic Mucosa	Colon
2	chr15:45002400-45006800	Active TSS	Small Intestine	intestine
3	chr15:45002400-45007000	Active TSS	Left Ventricle	heart
4	chr15:45002400-45007200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr15:45002400-45007200	Active TSS	Right Ventricle	heart
6	chr15:45002600-45007200	Active TSS	Psoas Muscle	Psoas
7	chr15:45003200-45011600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr15:45003800-45006800	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr15:45003800-45008200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
10	chr15:45003800-45010600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
11	chr15:45004000-45008400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:45004200-45007800	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
13	chr15:45004200-45012400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
14	chr15:45004400-45006800	Active TSS	Right Atrium	heart
15	chr15:45004400-45008600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:45004400-45009000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:45004400-45009400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
18	chr15:45004400-45009800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
19	chr15:45004600-45008400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:45004600-45020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:45004800-45008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:45004800-45008800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:45005000-45007200	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr15:45005000-45007600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr15:45005000-45007600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:45005000-45018400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:45005000-45018600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:45005200-45007600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:45005200-45007600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:45005200-45007600	Weak transcription	Pancreas	Pancrea
31	chr15:45005200-45007800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:45005200-45007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:45005200-45008000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:45005200-45008000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:45005200-45008400	Weak transcription	Fetal Brain Male	brain
36	chr15:45005200-45011400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
37	chr15:45005400-45006800	Enhancers	Stomach Mucosa	stomach
38	chr15:45005400-45006800	Transcr. at gene 5' and 3'	Hela-S3	cervix
39	chr15:45005400-45007000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:45005400-45007200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:45005400-45007400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:45005400-45007400	Weak transcription	Fetal Stomach	stomach
43	chr15:45005400-45007400	Weak transcription	Gastric	stomach
44	chr15:45005400-45007400	Weak transcription	Spleen	Spleen
45	chr15:45005400-45007600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:45005400-45007600	Weak transcription	Aorta	Aorta
47	chr15:45005400-45007600	Weak transcription	Fetal Kidney	kidney
48	chr15:45005400-45007800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:45005400-45007800	Weak transcription	Esophagus	oesophagus
50	chr15:45005400-45007800	Enhancers	Fetal Heart	heart

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