Variant report

Variant	rs11759478
Chromosome Location	chr6:15351708-15351709
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15339473..15343526-chr6:15347239..15351934,4	K562	blood:
2	chr12:133403501..133405469-chr6:15351577..15353994,2	MCF-7	breast:
3	chr6:15350348..15351999-chr6:15369721..15371306,2	MCF-7	breast:
4	chr6:15350037..15352732-chr6:15370116..15373857,3	K562	blood:
5	chr6:15350514..15352108-chr6:15353885..15356215,2	MCF-7	breast:
6	chr6:15350544..15352569-chr6:15377945..15380141,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090615	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10949292	0.84[EUR][1000 genomes]
rs10949294	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10949295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs11753952	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756544	0.88[JPT][hapmap]
rs11757415	0.88[JPT][hapmap]
rs12192599	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12198692	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12198694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12199895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12201889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12204124	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12206745	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12209228	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12209748	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12210592	1.00[CEU][hapmap]
rs12211278	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12211777	1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214719	0.84[EUR][1000 genomes]
rs12215596	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs12215740	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13192347	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13194410	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13195950	0.86[JPT][hapmap]
rs13205396	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13205612	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13208486	0.88[JPT][hapmap]
rs16876250	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16876278	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs16876354	0.88[JPT][hapmap]
rs17575737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17576233	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17576436	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17576710	0.88[JPT][hapmap]
rs17619730	0.82[CEU][hapmap]
rs17619838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs17637773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs17638192	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs17638720	0.88[JPT][hapmap]
rs17687211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17713010	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs2237146	0.88[JPT][hapmap]
rs2299051	0.88[JPT][hapmap]
rs55980198	0.83[AMR][1000 genomes]
rs58674331	0.82[AFR][1000 genomes]
rs6459405	0.85[YRI][hapmap]
rs6902997	0.93[AMR][1000 genomes]
rs6919296	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs6935879	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6938919	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs72834590	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs742102	0.88[JPT][hapmap]
rs7747437	0.88[JPT][hapmap]
rs7765425	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7767966	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15327800-15375800	Weak transcription	Aorta	Aorta
2	chr6:15332000-15355800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:15332000-15359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:15341000-15362800	Weak transcription	Fetal Intestine Small	intestine
5	chr6:15341200-15359400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:15341400-15365400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:15341600-15352200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:15341800-15352600	Weak transcription	Pancreas	Pancrea
9	chr6:15341800-15362800	Weak transcription	Gastric	stomach
10	chr6:15341800-15378400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:15342000-15351800	Weak transcription	HSMM	muscle
12	chr6:15342000-15352800	Weak transcription	Fetal Kidney	kidney
13	chr6:15342600-15352000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:15342600-15352600	Weak transcription	Stomach Mucosa	stomach
15	chr6:15342800-15352000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:15342800-15364600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:15343400-15353400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:15344800-15351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:15345400-15351800	Weak transcription	Fetal Stomach	stomach
20	chr6:15345600-15352800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:15345600-15357400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:15346200-15351800	Weak transcription	K562	blood
23	chr6:15347000-15352000	Weak transcription	Brain Germinal Matrix	brain
24	chr6:15347000-15355400	Enhancers	Primary T cells from cord blood	blood
25	chr6:15347600-15352800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:15348000-15352000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:15348600-15356000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:15348800-15353400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:15348800-15359000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:15348800-15360000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:15349000-15352200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:15349000-15352200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:15349000-15353200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:15349000-15353400	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:15349000-15353800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:15349000-15354200	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr6:15349000-15355000	Enhancers	Fetal Lung	lung
38	chr6:15349200-15353000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:15349200-15353200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr6:15349200-15353400	Enhancers	NHDF-Ad	bronchial
41	chr6:15349200-15355000	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:15349200-15359000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr6:15349400-15353600	Enhancers	Osteobl	bone
44	chr6:15349600-15351800	Weak transcription	Thymus	Thymus
45	chr6:15349600-15354600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:15349600-15360000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr6:15349800-15352200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr6:15349800-15358400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
49	chr6:15350200-15353600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:15350400-15352600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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