Variant report

Variant	rs6861539
Chromosome Location	chr5:178452307-178452308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178451565..178453293-chr5:178455866..178457677,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10479519	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10479520	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516149	0.95[ASN][1000 genomes]
rs10516150	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505147	0.82[ASN][1000 genomes]
rs11951738	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957976	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958355	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960161	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152869	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160086	0.86[ASN][1000 genomes]
rs13161528	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188724	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13359549	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359570	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359572	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361077	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17078988	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078991	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047354	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132671	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132672	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054398	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431447	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34881171	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35568336	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797615	0.86[ASN][1000 genomes]
rs4700780	0.94[ASN][1000 genomes]
rs4700781	0.88[ASN][1000 genomes]
rs4701030	0.95[ASN][1000 genomes]
rs4701045	0.88[ASN][1000 genomes]
rs58827878	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60061283	0.90[ASN][1000 genomes]
rs60073676	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62393072	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393074	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393075	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62393076	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601007	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601010	0.85[ASN][1000 genomes]
rs6859576	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859767	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860309	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867119	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867208	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868893	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875473	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875622	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880315	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888539	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6888567	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6890317	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7707587	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708743	0.92[ASN][1000 genomes]
rs7709054	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711420	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732719	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733072	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv883221	chr5:178410538-178454118	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6861539	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178451200-178461800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr5:178451400-178452400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:178451400-178452400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr5:178451400-178453800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:178451400-178453800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:178451400-178458000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:178451400-178461800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:178451600-178452400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:178451600-178452400	ZNF genes & repeats	A549	lung
10	chr5:178451600-178452600	ZNF genes & repeats	Pancreas	Pancrea
11	chr5:178451600-178452800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:178451600-178453200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:178451600-178453600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:178451600-178453800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:178451600-178454000	Weak transcription	HSMM	muscle
16	chr5:178451600-178456000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:178451600-178456000	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr5:178451600-178460600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr5:178451600-178461400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:178451600-178461800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr5:178451800-178452400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:178451800-178452400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr5:178451800-178452600	ZNF genes & repeats	Lung	lung
24	chr5:178451800-178453600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr5:178451800-178453600	Weak transcription	Aorta	Aorta
26	chr5:178451800-178453600	Weak transcription	HSMMtube	muscle
27	chr5:178451800-178453800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:178451800-178453800	Weak transcription	Colonic Mucosa	Colon
29	chr5:178451800-178453800	Weak transcription	Fetal Heart	heart
30	chr5:178451800-178453800	Weak transcription	Right Ventricle	heart
31	chr5:178451800-178453800	Weak transcription	NHEK	skin
32	chr5:178451800-178454000	Weak transcription	NHLF	lung
33	chr5:178451800-178454000	Weak transcription	Osteobl	bone
34	chr5:178451800-178456000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
35	chr5:178451800-178456000	ZNF genes & repeats	Fetal Intestine Large	intestine
36	chr5:178451800-178457800	Weak transcription	HUVEC	blood vessel
37	chr5:178451800-178460800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:178451800-178461800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:178451800-178461800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:178451800-178464000	ZNF genes & repeats	Liver	Liver
41	chr5:178452000-178452400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr5:178452000-178452400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:178452000-178452400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr5:178452000-178452600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:178452000-178452600	ZNF genes & repeats	Esophagus	oesophagus
46	chr5:178452000-178452800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:178452000-178453000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:178452000-178453000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:178452000-178453200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr5:178452000-178453200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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