Variant report

Variant	rs7350779
Chromosome Location	chr15:39725242-39725243
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39721051..39725636-chr15:39870055..39875310,7	MCF-7	breast:
2	chr15:39724781..39729630-chr15:39730304..39736268,5	MCF-7	breast:
3	chr15:39712002..39713506-chr15:39725005..39726661,2	MCF-7	breast:
4	chr15:39464240..39465905-chr15:39723603..39725817,2	MCF-7	breast:
5	chr15:39724107..39725948-chr15:39841990..39843603,2	MCF-7	breast:
6	chr15:39723566..39727788-chr15:39872507..39874775,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction
ENSG00000259345	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11070204	1.00[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1158918	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11633970	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857561	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438465	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593294	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899217	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1551945	0.82[MEX][hapmap]
rs16952151	0.82[MEX][hapmap]
rs16969038	0.82[MEX][hapmap]
rs1812583	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1947782	0.87[ASN][1000 genomes]
rs1993892	0.87[ASN][1000 genomes]
rs1993893	0.84[ASN][1000 genomes]
rs2086166	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2127029	1.00[CEU][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2411293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34329697	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244571	1.00[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4486853	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924361	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924363	0.87[ASN][1000 genomes]
rs5028679	0.82[MEX][hapmap]
rs59431794	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60697424	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171244	0.93[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7178351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74008200	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74010438	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8032900	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs8033214	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888722	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920539	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7350779	AQR	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39713200-39727400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr15:39719200-39728200	Enhancers	HUVEC	blood vessel
3	chr15:39719400-39726800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:39719600-39727200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr15:39720200-39725600	Weak transcription	Lung	lung
6	chr15:39720200-39726800	Weak transcription	Adipose Nuclei	Adipose
7	chr15:39720400-39726400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr15:39721800-39725400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:39722400-39727800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:39722600-39725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:39722600-39725600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:39722600-39726800	Weak transcription	Small Intestine	intestine
13	chr15:39722600-39727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:39722800-39725600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:39722800-39725600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:39722800-39730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:39723000-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:39723000-39726800	Weak transcription	Stomach Mucosa	stomach
19	chr15:39723000-39727000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:39723200-39725400	Weak transcription	Primary T cells from cord blood	blood
21	chr15:39723400-39725400	Weak transcription	Fetal Thymus	thymus
22	chr15:39723800-39725400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:39723800-39725400	Enhancers	Stomach Smooth Muscle	stomach
24	chr15:39723800-39727400	Enhancers	Colon Smooth Muscle	Colon
25	chr15:39723800-39731200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:39724000-39725600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:39724000-39725600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:39724000-39727000	Weak transcription	NH-A	brain
29	chr15:39724000-39728000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr15:39724200-39725800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr15:39724200-39727400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr15:39724200-39727400	Enhancers	Rectal Smooth Muscle	rectum
33	chr15:39724200-39727800	Enhancers	Fetal Muscle Leg	muscle
34	chr15:39724400-39726400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:39724600-39726800	Weak transcription	Osteobl	bone
36	chr15:39724600-39729800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:39724800-39725400	Enhancers	Fetal Heart	heart
38	chr15:39724800-39725800	Enhancers	Spleen	Spleen
39	chr15:39724800-39727400	Enhancers	Right Atrium	heart
40	chr15:39724800-39727800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr15:39725000-39725800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:39725000-39725800	Enhancers	Esophagus	oesophagus
43	chr15:39725000-39726200	Enhancers	Right Ventricle	heart
44	chr15:39725000-39726800	Enhancers	Thymus	Thymus
45	chr15:39725000-39727200	Enhancers	NHDF-Ad	bronchial
46	chr15:39725000-39728400	Enhancers	Fetal Stomach	stomach
47	chr15:39725000-39728800	Enhancers	HepG2	liver
48	chr15:39725200-39725400	Enhancers	Aorta	Aorta
49	chr15:39725200-39725400	Enhancers	HMEC	breast
50	chr15:39725200-39725600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links