Variant report

Variant	rs4409225
Chromosome Location	chr6:5502038-5502039
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12204848	0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs6597135	0.93[ASN][1000 genomes]
rs6597136	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6921688	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9328307	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9405840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9502311	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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:57 , 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	chr6:5472600-5506200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:5482200-5506600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:5485200-5506400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:5486000-5505400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:5486200-5506800	Weak transcription	Thymus	Thymus
12	chr6:5486400-5502800	Weak transcription	HepG2	liver
13	chr6:5488000-5510600	Weak transcription	Aorta	Aorta
14	chr6:5488200-5506200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:5488200-5506400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:5488600-5506000	Weak transcription	Primary B cells from cord blood	blood
17	chr6:5488600-5521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:5495400-5502400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:5495400-5505400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:5496200-5502200	Weak transcription	Psoas Muscle	Psoas
21	chr6:5498200-5502200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:5498400-5502200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:5498400-5506200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:5498800-5513000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:5499200-5502400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:5499400-5502200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:5499400-5502600	Enhancers	HSMMtube	muscle
28	chr6:5500000-5510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:5500200-5511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:5500400-5502200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:5500400-5507600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:5500400-5510600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:5500400-5511800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:5500400-5525000	Weak transcription	Spleen	Spleen
35	chr6:5500600-5508200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:5500600-5510600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr6:5500800-5502200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:5500800-5502200	Weak transcription	Left Ventricle	heart
39	chr6:5500800-5511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:5501000-5511800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
42	chr6:5501200-5505800	Weak transcription	Primary T cells from cord blood	blood
43	chr6:5501200-5511800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:5501400-5502200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:5501400-5502200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:5501400-5502200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:5501400-5502800	Enhancers	Fetal Heart	heart
48	chr6:5501400-5506600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr6:5501400-5506800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:5501400-5513400	Weak transcription	Brain Anterior Caudate	brain

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