Variant report

Variant	rs671470
Chromosome Location	chr18:12001419-12001420
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	chr18:11980409..11982733-chr18:12000463..12003199,2	MCF-7	breast:
2	chr18:12000492..12002135-chr18:12004782..12007391,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1249977	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1265916	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352114	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4555213	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606105	0.86[GIH][hapmap]
rs626097	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636173	0.81[CEU][hapmap];0.91[GIH][hapmap]
rs639457	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505704	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505705	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505706	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs663401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669838	0.81[CEU][hapmap]
rs672917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[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]
rs686961	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7234493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7244276	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7244661	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9955803	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9955982	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956089	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
3	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr18:11995400-12001800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr18:11995600-12014400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr18:11996000-12004000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr18:11996000-12004800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:11996000-12004800	Weak transcription	HMEC	breast
9	chr18:11996000-12005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:11996200-12004800	Weak transcription	NHEK	skin
11	chr18:11996200-12005200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr18:11996200-12005600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr18:11996200-12012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr18:11996200-12014800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr18:11996200-12015400	Weak transcription	Brain Anterior Caudate	brain
16	chr18:11996400-12002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr18:11996400-12004000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr18:11996400-12005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr18:11996400-12007800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr18:11996600-12005000	Weak transcription	GM12878-XiMat	blood
21	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
22	chr18:11996800-12017200	Weak transcription	Fetal Thymus	thymus
23	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
24	chr18:11997000-12004800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr18:11998400-12006000	Weak transcription	Brain Angular Gyrus	brain
27	chr18:11998400-12013200	Weak transcription	Right Atrium	heart
28	chr18:11998400-12014400	Weak transcription	Psoas Muscle	Psoas
29	chr18:11998400-12015200	Weak transcription	Brain Hippocampus Middle	brain
30	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr18:11998600-12002600	Enhancers	Stomach Mucosa	stomach
32	chr18:11998600-12005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr18:11998600-12010000	Weak transcription	Colon Smooth Muscle	Colon
34	chr18:11998800-12005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr18:11998800-12029400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:11999000-12002000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr18:11999000-12002600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr18:11999000-12002800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr18:11999000-12006800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr18:11999000-12017400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr18:11999000-12019200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:11999000-12019400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:11999000-12019400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr18:11999000-12034000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr18:11999200-12002000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr18:11999200-12002000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr18:11999200-12002000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr18:11999200-12002000	Strong transcription	Placenta	Placenta
50	chr18:11999200-12002600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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