Variant report

Variant	rs9405272
Chromosome Location	chr6:5501389-5501390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10458088	0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs10900969	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10900970	0.83[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11243014	0.83[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11243017	0.83[ASN][1000 genomes]
rs12527880	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs17140150	1.00[ASW][hapmap]
rs17140155	1.00[ASW][hapmap]
rs17140553	1.00[ASW][hapmap]
rs6935992	0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7763423	0.81[CHD][hapmap]
rs9328309	0.83[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs9378427	0.82[EUR][1000 genomes]
rs9378956	0.84[ASN][1000 genomes]
rs9378957	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9378958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378959	0.83[CHB][hapmap]
rs9405273	0.81[CHD][hapmap]
rs9405274	0.81[GIH][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr6:5461600-5507200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:5466400-5518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:5466600-5506400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:5466800-5502200	Weak transcription	Gastric	stomach
5	chr6:5471800-5505800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:5472400-5511600	Weak transcription	Fetal Stomach	stomach
7	chr6:5472600-5501800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:5472600-5506200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:5482200-5506600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:5485200-5506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:5486000-5505400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:5486200-5506800	Weak transcription	Thymus	Thymus
13	chr6:5486400-5502800	Weak transcription	HepG2	liver
14	chr6:5488000-5501800	Weak transcription	Liver	Liver
15	chr6:5488000-5510600	Weak transcription	Aorta	Aorta
16	chr6:5488200-5506200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:5488200-5506400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:5488600-5506000	Weak transcription	Primary B cells from cord blood	blood
19	chr6:5488600-5521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:5495400-5502400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr6:5495400-5505400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:5496200-5502200	Weak transcription	Psoas Muscle	Psoas
23	chr6:5498200-5502200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:5498400-5502200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:5498400-5506200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:5498600-5501400	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:5498800-5501400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:5498800-5501400	Enhancers	HSMM	muscle
29	chr6:5498800-5513000	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:5499000-5501400	Enhancers	NHEK	skin
31	chr6:5499000-5501600	Enhancers	Adipose Nuclei	Adipose
32	chr6:5499000-5501600	Enhancers	Osteobl	bone
33	chr6:5499200-5501400	Enhancers	HMEC	breast
34	chr6:5499200-5501600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:5499200-5502400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:5499400-5501400	Enhancers	Brain Angular Gyrus	brain
37	chr6:5499400-5501600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:5499400-5501600	Enhancers	Brain Substantia Nigra	brain
39	chr6:5499400-5501600	Enhancers	Right Ventricle	heart
40	chr6:5499400-5502200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:5499400-5502600	Enhancers	HSMMtube	muscle
42	chr6:5499600-5501400	Enhancers	Brain Anterior Caudate	brain
43	chr6:5499600-5501400	Enhancers	Brain Hippocampus Middle	brain
44	chr6:5499600-5501400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:5499600-5501600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:5499800-5501400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:5499800-5501600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:5499800-5501600	Enhancers	NHDF-Ad	bronchial
49	chr6:5500000-5501400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr6:5500000-5510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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