Variant report

Variant	rs17705279
Chromosome Location	chr19:35811336-35811337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:35758596..35761330-chr19:35808386..35811398,6	MCF-7	breast:
2	chr19:35808879..35811383-chr19:35819038..35823207,3	K562	blood:
3	chr19:35604701..35607129-chr19:35809231..35811359,2	MCF-7	breast:
4	chr12:41311476..41312055-chr19:35811147..35811765,2	MCF-7	breast:
5	chr19:35755149..35764508-chr19:35799437..35813142,44	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089356	Chromatin interaction
ENSG00000269553	Chromatin interaction
ENSG00000105699	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000012124	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11666282	0.84[CEU][hapmap]
rs11670792	0.89[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs11673522	0.84[CEU][hapmap]
rs12461927	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12463142	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17637981	0.94[CEU][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1811170	0.97[EUR][1000 genomes]
rs2285447	0.88[EUR][1000 genomes]
rs720308	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs720309	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs73031717	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17705279	CYP2B7P1	cis	parietal	SCAN
rs17705279	SLAIN1	trans	lymphoblastoid	seeQTL
rs17705279	PSMC4	cis	cerebellum	SCAN
rs17705279	HIPK4	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35798200-35811400	Weak transcription	Liver	Liver
2	chr19:35805600-35811400	Enhancers	K562	blood
3	chr19:35807800-35812000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr19:35807800-35815800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr19:35808000-35812200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:35808000-35812800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:35808200-35812000	Enhancers	Placenta	Placenta
8	chr19:35808400-35812000	Enhancers	Spleen	Spleen
9	chr19:35808600-35811600	Enhancers	Fetal Muscle Trunk	muscle
10	chr19:35808600-35812000	Enhancers	Brain Cingulate Gyrus	brain
11	chr19:35809400-35811600	Enhancers	NHDF-Ad	bronchial
12	chr19:35809400-35812000	Enhancers	Brain Substantia Nigra	brain
13	chr19:35809400-35812200	Enhancers	Brain Hippocampus Middle	brain
14	chr19:35809600-35811600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr19:35809600-35812000	Enhancers	Brain Angular Gyrus	brain
16	chr19:35809600-35812200	Enhancers	GM12878-XiMat	blood
17	chr19:35809800-35811800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr19:35809800-35812000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr19:35809800-35812200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr19:35810000-35812000	Enhancers	Brain Anterior Caudate	brain
21	chr19:35810000-35812000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr19:35810000-35812200	Enhancers	Primary hematopoietic stem cells	blood
23	chr19:35810200-35811400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:35810200-35811400	Weak transcription	Ovary	ovary
25	chr19:35810400-35811400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:35810400-35811400	Weak transcription	Lung	lung
27	chr19:35810400-35811800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:35810400-35811800	Enhancers	Adipose Nuclei	Adipose
29	chr19:35810400-35835200	Weak transcription	Fetal Lung	lung
30	chr19:35810600-35811600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr19:35810600-35817000	Weak transcription	HepG2	liver
32	chr19:35811000-35811400	Flanking Active TSS	Primary B cells from peripheral blood	blood
33	chr19:35811000-35811400	Enhancers	Fetal Thymus	thymus
34	chr19:35811000-35811600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:35811000-35811600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:35811000-35811800	Enhancers	Right Ventricle	heart
37	chr19:35811000-35811800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr19:35811200-35812000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links