Variant report

Variant	rs1077809
Chromosome Location	chr15:41804694-41804695
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	SUZ12	chr15:41803702-41806103	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41801767..41805579-chr15:41951979..41954300,3	K562	blood:
2	chr15:41803642..41805353-chr15:41818402..41820685,2	K562	blood:

Variant related genes	Relation type
LTK	TF binding region
ENSG00000103932	Chromatin interaction
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10851405	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070331	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1200340	0.89[EUR][1000 genomes]
rs1200345	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs1200348	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs1200349	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs1867419	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2253936	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274858	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs2289739	0.87[GIH][hapmap]
rs2289740	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2297377	0.84[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2297378	0.81[CHB][hapmap]
rs2777490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316622	0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.93[ASN][1000 genomes]
rs316623	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3759793	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8035331	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8035575	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv904110	chr15:41776692-41813279	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv904111	chr15:41777898-41805115	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv471241	chr15:41783814-41820200	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv569233	chr15:41784809-41805237	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv33378	chr15:41786505-41805760	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1077809	TYRO3	cis	parietal	SCAN
rs1077809	SPTBN5	cis	parietal	SCAN
rs1077809	BUB1B	cis	parietal	SCAN
rs1077809	RPAP1	cis	parietal	SCAN
rs1077809	LTK	cis	lung	GTEx
rs1077809	NDUFAF1	cis	lymphoblastoid	seeQTL
rs1077809	SPINT1	cis	parietal	SCAN
rs1077809	NDUFAF1	cis	parietal	SCAN
rs1077809	RPAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41801800-41819000	Weak transcription	Hela-S3	cervix
2	chr15:41803000-41804800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:41803200-41806400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr15:41803200-41806400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:41803400-41804800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:41803400-41804800	Active TSS	Gastric	stomach
7	chr15:41803400-41804800	Weak transcription	K562	blood
8	chr15:41803400-41805000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:41803400-41806200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:41803400-41806400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:41803600-41804800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:41803600-41805000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr15:41803600-41805000	Enhancers	Lung	lung
14	chr15:41803600-41805400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
15	chr15:41803600-41805400	Bivalent Enhancer	Fetal Heart	heart
16	chr15:41803600-41805600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
17	chr15:41803600-41806000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr15:41803600-41806200	Bivalent Enhancer	Fetal Brain Male	brain
19	chr15:41803600-41806200	Enhancers	Pancreas	Pancrea
20	chr15:41803600-41806200	Bivalent Enhancer	HMEC	breast
21	chr15:41803600-41806400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:41803800-41804800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
23	chr15:41803800-41804800	Bivalent Enhancer	Spleen	Spleen
24	chr15:41803800-41805000	Bivalent Enhancer	Esophagus	oesophagus
25	chr15:41803800-41806200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:41803800-41806400	Bivalent Enhancer	Fetal Thymus	thymus
27	chr15:41804000-41805600	Bivalent/Poised TSS	Psoas Muscle	Psoas
28	chr15:41804000-41806200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
29	chr15:41804000-41806200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
30	chr15:41804000-41806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:41804000-41806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:41804000-41806400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
33	chr15:41804200-41804800	Bivalent/Poised TSS	HepG2	liver
34	chr15:41804200-41805000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:41804200-41805000	Bivalent/Poised TSS	HSMM	muscle
36	chr15:41804200-41805200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
37	chr15:41804200-41805200	Bivalent Enhancer	Left Ventricle	heart
38	chr15:41804200-41805400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:41804200-41805800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
40	chr15:41804200-41805800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
41	chr15:41804200-41806000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:41804200-41806200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
43	chr15:41804200-41806200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
44	chr15:41804200-41806200	Flanking Active TSS	Ovary	ovary
45	chr15:41804200-41806200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
47	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
48	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
49	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:41804200-41806400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle

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