Variant report

Variant	rs935886
Chromosome Location	chr15:45013398-45013399
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44967397..44969275-chr15:45011739..45013954,2	K562	blood:
2	chr15:45010137..45014339-chr15:45017544..45021915,6	MCF-7	breast:
3	chr15:45007100..45009716-chr15:45011115..45014143,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229474	Chromatin interaction
ENSG00000166710	Chromatin interaction
ENSG00000185880	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1060392	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1295358	0.85[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs14711	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901534	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2254831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254835	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]
rs2290330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[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];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3100142	1.00[CEU][hapmap];0.80[AMR][1000 genomes];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];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3110173	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3110174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3110176	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3110182	0.85[EUR][1000 genomes]
rs3110662	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3110675	0.84[EUR][1000 genomes]
rs6493108	0.92[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];0.94[ASN][1000 genomes]
rs7165535	0.80[MEX][hapmap]
rs7172083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs935886	TRIM69	cis	Frontal Cortex	GTEx
rs935886	CHST14	cis	parietal	SCAN
rs935886	TRIM69	cis	cerebellum	SCAN
rs935886	TRIM69	cis	Esophagus Muscularis	GTEx
rs935886	TRIM69	cis	Artery Tibial	GTEx
rs935886	TRIM69	cis	parietal	SCAN
rs935886	TRIM69	cis	Adipose Subcutaneous	GTEx
rs935886	CHP	cis	cerebellum	SCAN
rs935886	TRIM69	cis	Muscle Skeletal	GTEx

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	chr15:45008200-45013400	Genic enhancers	Primary B cells from cord blood	blood
5	chr15:45008600-45018400	Weak transcription	A549	lung
6	chr15:45008800-45018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:45009000-45013400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:45009000-45018200	Weak transcription	Stomach Mucosa	stomach
9	chr15:45009000-45018400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:45009000-45018400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:45009000-45018400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:45009400-45017600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:45009400-45018400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:45009400-45018600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:45009400-45020000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:45009400-45020600	Weak transcription	Brain Angular Gyrus	brain
17	chr15:45009400-45020600	Weak transcription	Pancreas	Pancrea
18	chr15:45009400-45020600	Weak transcription	Right Ventricle	heart
19	chr15:45009400-45020800	Weak transcription	Aorta	Aorta
20	chr15:45009600-45018200	Weak transcription	NHEK	skin
21	chr15:45009600-45018400	Weak transcription	Esophagus	oesophagus
22	chr15:45009600-45020600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:45009600-45020800	Weak transcription	Fetal Brain Male	brain
24	chr15:45009800-45017600	Weak transcription	Small Intestine	intestine
25	chr15:45009800-45018400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:45010200-45018400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:45010200-45020600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:45010200-45020600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:45010200-45020600	Weak transcription	Fetal Kidney	kidney
30	chr15:45010400-45018400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:45010400-45018400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:45010600-45015200	Weak transcription	K562	blood
33	chr15:45010600-45018200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:45010600-45018400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:45010600-45018400	Weak transcription	Colonic Mucosa	Colon
36	chr15:45010600-45020200	Weak transcription	Psoas Muscle	Psoas
37	chr15:45010600-45020600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr15:45010600-45020600	Weak transcription	Brain Substantia Nigra	brain
39	chr15:45010800-45018400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:45010800-45018600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:45010800-45020600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:45010800-45020600	Weak transcription	Ovary	ovary
43	chr15:45011000-45017600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr15:45011000-45017800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:45011000-45019000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:45011000-45020600	Weak transcription	Brain Hippocampus Middle	brain
47	chr15:45011000-45020600	Weak transcription	Fetal Stomach	stomach
48	chr15:45011200-45016400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr15:45011200-45017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:45011200-45018400	Weak transcription	HMEC	breast

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