Variant report

Variant	rs1738288
Chromosome Location	chr6:128588247-128588248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10485161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10485162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11962214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11962916	1.00[CHB][hapmap]
rs11968433	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11970637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12110357	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1339188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1538498	1.00[CEU][hapmap]
rs1543376	1.00[CEU][hapmap]
rs17053270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17055445	1.00[CHB][hapmap]
rs17055450	1.00[CEU][hapmap]
rs17055452	1.00[CEU][hapmap]
rs17055488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17055499	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17055501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17055507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17055628	1.00[CEU][hapmap]
rs17055630	1.00[CEU][hapmap]
rs17055679	1.00[CEU][hapmap]
rs1738273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1738283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768346	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768347	1.00[CEU][hapmap]
rs1768353	1.00[CEU][hapmap]
rs1768357	1.00[CEU][hapmap]
rs1768358	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1856498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813371	1.00[CEU][hapmap]
rs3813373	1.00[CEU][hapmap]
rs3923033	0.80[EUR][1000 genomes]
rs4421217	1.00[CEU][hapmap]
rs4440487	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4897252	1.00[CEU][hapmap]
rs6900798	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6905735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6910587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6913718	1.00[CEU][hapmap]
rs6913738	1.00[CHB][hapmap]
rs6928143	1.00[CEU][hapmap]
rs6933133	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6938118	1.00[CEU][hapmap]
rs73590658	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7746783	0.81[ASN][1000 genomes]
rs7751187	1.00[CHB][hapmap]
rs7754321	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7754637	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7755836	1.00[CEU][hapmap]
rs7769070	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7772941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773849	1.00[CEU][hapmap]
rs7776405	1.00[CEU][hapmap]
rs9372885	1.00[CEU][hapmap]
rs9375550	1.00[CEU][hapmap]
rs9388626	1.00[CEU][hapmap]
rs9402024	1.00[CEU][hapmap]
rs9784880	1.00[CEU][hapmap]
rs981998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128555600-128595800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:128564400-128588600	Weak transcription	NHEK	skin
3	chr6:128568000-128592000	Weak transcription	Brain Angular Gyrus	brain
4	chr6:128571200-128596200	Weak transcription	HSMMtube	muscle
5	chr6:128574000-128592200	Weak transcription	Gastric	stomach
6	chr6:128574000-128596200	Weak transcription	HSMM	muscle
7	chr6:128574400-128592600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:128574600-128596400	Weak transcription	NH-A	brain
9	chr6:128580000-128589000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:128580000-128592400	Weak transcription	Right Ventricle	heart
11	chr6:128580400-128592000	Weak transcription	Small Intestine	intestine
12	chr6:128581200-128592600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:128581600-128592600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:128582000-128592200	Weak transcription	Osteobl	bone
15	chr6:128582000-128596200	Weak transcription	NHDF-Ad	bronchial
16	chr6:128583200-128592600	Weak transcription	Thymus	Thymus
17	chr6:128584400-128589200	Weak transcription	Placenta	Placenta
18	chr6:128584400-128592200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr6:128584400-128592200	Weak transcription	Left Ventricle	heart
20	chr6:128585200-128591800	Weak transcription	Liver	Liver
21	chr6:128585200-128592400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:128585200-128592400	Weak transcription	Fetal Stomach	stomach
23	chr6:128585200-128596200	Weak transcription	HMEC	breast
24	chr6:128585200-128617600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:128585400-128592200	Weak transcription	Fetal Thymus	thymus
26	chr6:128585400-128592400	Weak transcription	Pancreas	Pancrea
27	chr6:128585400-128598200	Weak transcription	HepG2	liver
28	chr6:128586000-128588400	Weak transcription	Primary T cells from cord blood	blood
29	chr6:128586200-128589000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:128586400-128602000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:128587000-128590400	Weak transcription	Ovary	ovary
32	chr6:128587000-128592400	Weak transcription	Stomach Mucosa	stomach
33	chr6:128587400-128589000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:128587400-128592400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:128587600-128588600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:128587600-128588800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:128587600-128592600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:128587600-128602200	Weak transcription	Fetal Intestine Large	intestine
39	chr6:128587800-128588600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:128587800-128588600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:128588000-128588600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:128588000-128589600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr6:128588000-128590000	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:128588000-128592400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:128588000-128592400	Weak transcription	Brain Anterior Caudate	brain
46	chr6:128588000-128608200	Weak transcription	Aorta	Aorta
47	chr6:128588200-128588400	Enhancers	HUVEC	blood vessel
48	chr6:128588200-128589000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:128588200-128589200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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