Variant report

Variant	rs16959544
Chromosome Location	chr17:16058348-16058349
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16057635..16060524-chr17:16061549..16064453,2	MCF-7	breast:
2	chr17:16056755..16059055-chr17:16074181..16076719,2	MCF-7	breast:
3	chr17:16056577..16058620-chr17:16118032..16120275,2	MCF-7	breast:
4	chr17:16052098..16053790-chr17:16057449..16059169,2	K562	blood:

Variant related genes	Relation type
ENSG00000141027	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1073093	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs1073094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1073095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs1076423	0.88[TSI][hapmap]
rs1076424	0.88[TSI][hapmap]
rs16959491	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs16959547	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][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]
rs17715109	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs2302314	0.85[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs3744328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs3760295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs4500784	0.81[AMR][1000 genomes]
rs4792723	0.90[AMR][1000 genomes]
rs56733317	0.87[ASN][1000 genomes]
rs57825293	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57843678	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58475330	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59172522	0.84[AMR][1000 genomes]
rs60011951	0.87[ASN][1000 genomes]
rs60918926	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61352879	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6502483	0.85[MEX][hapmap]
rs6502495	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6502496	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207630	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7207901	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7208681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7209811	0.85[CHD][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7210068	0.89[EUR][1000 genomes]
rs7210264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7211957	0.81[AMR][1000 genomes]
rs7212326	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7212874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7215673	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7217418	0.89[EUR][1000 genomes]
rs7218342	0.82[EUR][1000 genomes]
rs7219263	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7219365	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7219795	1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7219980	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7220699	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7223409	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7223807	0.82[EUR][1000 genomes]
rs7224403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7224575	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7225813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7225926	1.00[JPT][hapmap]
rs73978817	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73981431	0.84[AMR][1000 genomes]
rs73981433	0.84[AMR][1000 genomes]
rs73981436	0.84[AMR][1000 genomes]
rs73981440	0.84[ASN][1000 genomes]
rs73981442	0.84[ASN][1000 genomes]
rs73981443	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73981444	0.84[ASN][1000 genomes]
rs73981445	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73981447	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73981450	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73981453	0.81[AMR][1000 genomes]
rs73981460	0.81[AMR][1000 genomes]
rs73981461	0.81[AMR][1000 genomes]
rs73981462	0.90[AMR][1000 genomes]
rs73981464	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73981466	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981467	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981471	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73981482	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs764984	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs8065649	1.00[JPT][hapmap]
rs8067494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs8068335	0.89[EUR][1000 genomes]
rs8069052	0.89[EUR][1000 genomes]
rs8070719	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8077373	0.82[MEX][hapmap]
rs8077949	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8079698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes]
rs8079763	0.88[TSI][hapmap]
rs9674583	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1062220	chr17:15869557-16093156	Genic enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv1064878	chr17:15869557-16097241	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1055173	chr17:15875935-16097241	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv1056157	chr17:15890584-16088473	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv833377	chr17:15912013-16104515	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv522169	chr17:15923709-16147821	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv907711	chr17:15978663-16092902	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv907712	chr17:15981874-16103426	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv907713	chr17:15981874-16127206	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv907714	chr17:15990013-16110384	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16006600-16064200	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr17:16015600-16077600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr17:16015800-16064400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr17:16016400-16064200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr17:16017200-16064200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:16019400-16070400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr17:16020200-16064200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:16021800-16087600	Weak transcription	Fetal Brain Male	brain
9	chr17:16022200-16058400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr17:16032800-16058400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr17:16034800-16058600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr17:16034800-16061800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:16035400-16064600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:16035800-16103400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr17:16036800-16059800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:16039200-16096800	Weak transcription	K562	blood
17	chr17:16039400-16059000	Weak transcription	Stomach Mucosa	stomach
18	chr17:16041200-16059800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr17:16041200-16063200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:16042000-16094200	Weak transcription	Psoas Muscle	Psoas
21	chr17:16042600-16060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:16043400-16065800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr17:16043600-16064400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:16044000-16059200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr17:16045200-16069800	Strong transcription	Dnd41	blood
26	chr17:16046800-16059800	Weak transcription	Fetal Heart	heart
27	chr17:16046800-16064600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr17:16047800-16058800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr17:16048400-16064000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr17:16048400-16088000	Weak transcription	Fetal Brain Female	brain
31	chr17:16049200-16058400	Strong transcription	Fetal Lung	lung
32	chr17:16049200-16059000	Weak transcription	Pancreas	Pancrea
33	chr17:16049200-16063600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:16049200-16077600	Weak transcription	Right Ventricle	heart
35	chr17:16049200-16088600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:16049200-16093200	Weak transcription	Aorta	Aorta
37	chr17:16049200-16103400	Weak transcription	Spleen	Spleen
38	chr17:16049200-16108600	Weak transcription	Esophagus	oesophagus
39	chr17:16049400-16062000	Weak transcription	Brain Substantia Nigra	brain
40	chr17:16049400-16062400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr17:16049400-16064200	Strong transcription	Primary T cells from cord blood	blood
42	chr17:16049600-16058400	Strong transcription	HSMM	muscle
43	chr17:16049600-16058600	Strong transcription	Adipose Nuclei	Adipose
44	chr17:16050000-16058400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:16050800-16063000	Strong transcription	GM12878-XiMat	blood
46	chr17:16050800-16064200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr17:16051800-16059200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:16051800-16073800	Weak transcription	Left Ventricle	heart
49	chr17:16051800-16089400	Weak transcription	Brain Germinal Matrix	brain
50	chr17:16052000-16060800	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links