Variant report

Variant	rs1738278
Chromosome Location	chr6:128580323-128580324
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128566524..128568346-chr6:128578844..128580806,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11968696	0.81[AFR][1000 genomes]
rs1339188	0.81[LWK][hapmap];1.00[MEX][hapmap]
rs1738276	0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738277	0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738279	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738286	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1738291	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs1768348	0.87[AMR][1000 genomes]
rs1768349	0.87[AMR][1000 genomes]
rs1768350	0.87[AMR][1000 genomes]
rs1768352	1.00[MEX][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs1768353	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs1768356	1.00[AMR][1000 genomes]
rs1768357	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes]
rs1768359	0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4483000	0.92[MKK][hapmap]
rs55958764	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6900798	1.00[MEX][hapmap]
rs73592688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73592691	1.00[AMR][1000 genomes]
rs73592692	0.87[AFR][1000 genomes]
rs73594656	0.87[AMR][1000 genomes]
rs73594682	0.87[AMR][1000 genomes]
rs73596645	0.87[AMR][1000 genomes]
rs73596648	0.87[AMR][1000 genomes]
rs73596649	0.87[AMR][1000 genomes]
rs73596651	0.87[AMR][1000 genomes]
rs73596654	0.87[AMR][1000 genomes]
rs73596659	0.87[AMR][1000 genomes]
rs73596661	0.87[AMR][1000 genomes]
rs73772021	1.00[AMR][1000 genomes]
rs981998	1.00[MEX][hapmap]
rs981999	0.91[ASW][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs982000	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs982001	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs982002	0.90[ASW][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes]

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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128551400-128584400	Weak transcription	Pancreas	Pancrea
2	chr6:128555200-128584400	Weak transcription	HMEC	breast
3	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:128561400-128587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:128562800-128588200	Weak transcription	HUVEC	blood vessel
6	chr6:128563000-128585400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:128564400-128583400	Weak transcription	HepG2	liver
8	chr6:128564400-128588600	Weak transcription	NHEK	skin
9	chr6:128568000-128592000	Weak transcription	Brain Angular Gyrus	brain
10	chr6:128571200-128584200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:128571200-128596200	Weak transcription	HSMMtube	muscle
12	chr6:128574000-128588200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:128574000-128592200	Weak transcription	Gastric	stomach
14	chr6:128574000-128596200	Weak transcription	HSMM	muscle
15	chr6:128574200-128580600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:128574400-128592600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:128574600-128596400	Weak transcription	NH-A	brain
18	chr6:128574800-128584800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:128574800-128587200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:128575000-128585000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:128575200-128580400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:128576400-128584200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:128577400-128584000	Weak transcription	Fetal Intestine Small	intestine
24	chr6:128577600-128580400	Weak transcription	Fetal Heart	heart
25	chr6:128577600-128584200	Weak transcription	Liver	Liver
26	chr6:128577800-128584800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:128579400-128580400	Enhancers	Primary T cells from cord blood	blood
28	chr6:128579400-128580600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:128579600-128580400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:128579600-128580400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr6:128579600-128580400	Active TSS	NHDF-Ad	bronchial
32	chr6:128579600-128580600	Enhancers	Fetal Thymus	thymus
33	chr6:128579800-128580400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:128579800-128580400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:128579800-128580400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:128579800-128580400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:128579800-128580400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr6:128579800-128580400	Enhancers	Psoas Muscle	Psoas
39	chr6:128579800-128580400	Enhancers	Small Intestine	intestine
40	chr6:128579800-128580600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:128579800-128580600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:128579800-128580600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:128579800-128580600	Enhancers	Duodenum Mucosa	Duodenum
44	chr6:128579800-128580800	Enhancers	Primary hematopoietic stem cells	blood
45	chr6:128579800-128581400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr6:128580000-128580400	Enhancers	Primary B cells from cord blood	blood
47	chr6:128580000-128580400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:128580000-128580400	Enhancers	Esophagus	oesophagus
49	chr6:128580000-128580400	Enhancers	GM12878-XiMat	blood
50	chr6:128580000-128580600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links