Variant report

Variant	rs7165535
Chromosome Location	chr15:45016345-45016346
allele	A/G
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	JUN	chr15:45016303-45017301	K562	blood:	n/a	n/a
2	TBL1XR1	chr15:45016319-45017178	K562	blood:	n/a	n/a
3	SPI1	chr15:45016276-45017452	GM12878	blood:	n/a	chr15:45016996-45017005 chr15:45016997-45017004
4	REST	chr15:45016155-45016899	HL-60	blood:	n/a	chr15:45016410-45016430
5	PML	chr15:45016340-45017280	GM12878	blood:	n/a	n/a
6	FOXM1	chr15:45016333-45017026	GM12878	blood:	n/a	n/a
7	NFIC	chr15:45016251-45017397	GM12878	blood:	n/a	n/a
8	IRF1	chr15:45016299-45017211	K562	blood:	n/a	n/a
9	EP300	chr15:45016321-45017190	GM12878	blood:	n/a	chr15:45016996-45017005 chr15:45017054-45017061 chr15:45016446-45016460
10	CEBPB	chr15:45016244-45017063	K562	blood:	n/a	chr15:45016765-45016776 chr15:45016616-45016633 chr15:45016618-45016630
11	NFIC	chr15:45016344-45017263	GM12878	blood:	n/a	n/a
12	ZNF384	chr15:45016262-45017223	GM12878	blood:	n/a	n/a
13	CUX1	chr15:45016292-45016785	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45003079..45005012-chr15:45015823..45018860,3	MCF-7	breast:
2	chr15:44953449..44956958-chr15:45014890..45017031,3	K562	blood:
3	chr15:44953895..44957741-chr15:45015371..45022655,19	K562	blood:

Variant related genes	Relation type
TRIM69	TF binding region
ENSG00000104133	Chromatin interaction
ENSG00000166710	Chromatin interaction
ENSG00000229474	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10163110	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs10444818	0.93[ASN][1000 genomes]
rs1137516	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs11634059	0.92[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11634063	0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11639157	0.92[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12912870	0.85[ASN][1000 genomes]
rs1690313	0.82[CHB][hapmap]
rs1720725	1.00[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1720726	0.86[EUR][1000 genomes]
rs1869125	0.82[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs1901530	0.82[CHB][hapmap]
rs1901538	0.90[ASN][1000 genomes]
rs1993152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1993153	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2084835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2123149	0.90[CEU][hapmap]
rs2123150	0.81[EUR][1000 genomes]
rs2167595	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs2254835	0.80[MEX][hapmap]
rs2290331	0.80[MEX][hapmap]
rs2444003	0.80[MEX][hapmap]
rs2444009	0.80[MEX][hapmap]
rs2468067	0.93[ASN][1000 genomes]
rs2470908	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2960206	1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs3100140	0.92[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3100141	0.92[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3100143	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3110677	0.94[ASN][1000 genomes]
rs3759878	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3759881	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4923989	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs4923990	0.97[ASN][1000 genomes]
rs4923991	0.94[ASN][1000 genomes]
rs4923993	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs6416439	0.97[ASN][1000 genomes]
rs6416440	0.82[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs6493110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6493111	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6493112	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493114	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs6493116	0.94[ASN][1000 genomes]
rs6493118	1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs6493119	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs6493124	0.89[ASN][1000 genomes]
rs6493125	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7168090	0.90[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs7172376	0.94[ASN][1000 genomes]
rs7175483	0.82[EUR][1000 genomes]
rs7496437	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs7497862	0.80[ASN][1000 genomes]
rs8035787	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs8036223	0.97[ASN][1000 genomes]
rs935885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs935886	0.80[MEX][hapmap]
rs935888	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs935889	0.92[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7165535	TRIM69	Cis_1M	lymphoblastoid	RTeQTL
rs7165535	METT5D1	trans	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45004600-45020600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:45005000-45018400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:45005000-45018600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:45008600-45018400	Weak transcription	A549	lung
5	chr15:45008800-45018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:45009000-45018200	Weak transcription	Stomach Mucosa	stomach
7	chr15:45009000-45018400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:45009000-45018400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:45009000-45018400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:45009400-45017600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:45009400-45018400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:45009400-45018600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:45009400-45020000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:45009400-45020600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:45009400-45020600	Weak transcription	Pancreas	Pancrea
16	chr15:45009400-45020600	Weak transcription	Right Ventricle	heart
17	chr15:45009400-45020800	Weak transcription	Aorta	Aorta
18	chr15:45009600-45018200	Weak transcription	NHEK	skin
19	chr15:45009600-45018400	Weak transcription	Esophagus	oesophagus
20	chr15:45009600-45020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:45009600-45020800	Weak transcription	Fetal Brain Male	brain
22	chr15:45009800-45017600	Weak transcription	Small Intestine	intestine
23	chr15:45009800-45018400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:45010200-45018400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:45010200-45020600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:45010200-45020600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:45010200-45020600	Weak transcription	Fetal Kidney	kidney
28	chr15:45010400-45018400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:45010400-45018400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:45010600-45018200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:45010600-45018400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:45010600-45018400	Weak transcription	Colonic Mucosa	Colon
33	chr15:45010600-45020200	Weak transcription	Psoas Muscle	Psoas
34	chr15:45010600-45020600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:45010600-45020600	Weak transcription	Brain Substantia Nigra	brain
36	chr15:45010800-45018400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:45010800-45018600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:45010800-45020600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:45010800-45020600	Weak transcription	Ovary	ovary
40	chr15:45011000-45017600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr15:45011000-45017800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:45011000-45019000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr15:45011000-45020600	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:45011000-45020600	Weak transcription	Fetal Stomach	stomach
45	chr15:45011200-45016400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr15:45011200-45017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:45011200-45018400	Weak transcription	HMEC	breast
48	chr15:45011200-45018600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:45011200-45018600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:45011200-45018600	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links