Variant report

Variant	rs11079796
Chromosome Location	chr17:45903554-45903555
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45902742..45905383-chr17:45921555..45923450,2	MCF-7	breast:
2	chr17:45894310..45903569-chr17:45906761..45911816,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141294	Chromatin interaction
ENSG00000159111	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1005655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11079795	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11650289	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11650536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11652439	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11869958	0.95[CHB][hapmap]
rs11870002	0.95[CHB][hapmap]
rs16948401	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16948590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16948722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985407	0.89[CHB][hapmap]
rs2001381	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs2074188	0.95[CHB][hapmap]
rs2074189	0.95[CHB][hapmap]
rs3809869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs701984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72833426	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs878171	0.86[CHB][hapmap]
rs9674817	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription 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 miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11079796	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs11079796	OSBPL7	cis	Thyroid	GTEx
rs11079796	RPL27	cis	cerebellum	SCAN
rs11079796	CALCOCO2	cis	parietal	SCAN
rs11079796	VAT1	cis	cerebellum	SCAN
rs11079796	SCRN2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45899600-45903800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr17:45899800-45904000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:45899800-45904400	Weak transcription	Small Intestine	intestine
4	chr17:45899800-45908000	Weak transcription	Right Atrium	heart
5	chr17:45900200-45906400	Strong transcription	Fetal Intestine Small	intestine
6	chr17:45900200-45906800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:45900200-45907000	Strong transcription	Primary T cells from cord blood	blood
8	chr17:45900400-45903600	Weak transcription	Stomach Mucosa	stomach
9	chr17:45900400-45904000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:45900400-45904400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:45900400-45905800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:45900400-45906200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:45900400-45906200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:45900400-45906200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr17:45900400-45906200	Strong transcription	Brain Hippocampus Middle	brain
16	chr17:45900400-45906400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr17:45900400-45906400	Strong transcription	Liver	Liver
18	chr17:45900400-45906400	Strong transcription	Brain Germinal Matrix	brain
19	chr17:45900400-45906400	Strong transcription	Fetal Intestine Large	intestine
20	chr17:45900400-45906400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr17:45900400-45907200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr17:45900400-45907400	Weak transcription	Fetal Heart	heart
23	chr17:45900400-45907400	Strong transcription	Fetal Stomach	stomach
24	chr17:45900600-45903600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr17:45900600-45903600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:45900600-45905600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:45900600-45906200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:45900600-45906200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr17:45900600-45906200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:45900600-45906200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr17:45900600-45906200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr17:45900600-45906200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr17:45900600-45906200	Strong transcription	Brain Anterior Caudate	brain
34	chr17:45900600-45906200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:45900600-45906200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr17:45900600-45906200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:45900600-45906200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr17:45900600-45906200	Strong transcription	Spleen	Spleen
39	chr17:45900600-45906400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr17:45900600-45906400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:45900600-45906400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr17:45900600-45906400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr17:45900600-45906400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr17:45900600-45906400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr17:45900600-45906400	Strong transcription	Adipose Nuclei	Adipose
46	chr17:45900600-45906400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr17:45900600-45906400	Strong transcription	Placenta	Placenta
48	chr17:45900600-45906400	Strong transcription	Fetal Thymus	thymus
49	chr17:45900600-45906400	Strong transcription	Lung	lung
50	chr17:45900600-45906600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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