Variant report

Variant	rs9405840
Chromosome Location	chr6:5507182-5507183
allele	A/G
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];0.89[ASN][1000 genomes]
rs4409225	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]
rs6597135	0.90[ASN][1000 genomes]
rs6597136	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6921688	0.91[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9328307	0.92[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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:59 , 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	chr6:5472400-5511600	Weak transcription	Fetal Stomach	stomach
4	chr6:5488000-5510600	Weak transcription	Aorta	Aorta
5	chr6:5488600-5521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr6:5498800-5513000	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:5500000-5510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:5500200-5511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:5500400-5507600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:5500400-5510600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:5500400-5511800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:5500400-5525000	Weak transcription	Spleen	Spleen
13	chr6:5500600-5508200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:5500600-5510600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr6:5500800-5511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:5501000-5511800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
18	chr6:5501200-5511800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:5501400-5513400	Weak transcription	Brain Anterior Caudate	brain
20	chr6:5501600-5509000	Weak transcription	Right Ventricle	heart
21	chr6:5502400-5508600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:5502400-5511200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:5502400-5511200	Weak transcription	Gastric	stomach
24	chr6:5502600-5508600	Weak transcription	Left Ventricle	heart
25	chr6:5502800-5507400	Weak transcription	Fetal Heart	heart
26	chr6:5503200-5510600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:5505600-5507200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr6:5505600-5507200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:5505800-5507600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:5505800-5509000	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:5506000-5508200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:5506200-5507600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:5506200-5508000	Enhancers	Fetal Kidney	kidney
34	chr6:5506200-5508200	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr6:5506200-5508200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr6:5506200-5508400	Flanking Active TSS	GM12878-XiMat	blood
37	chr6:5506200-5509000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr6:5506400-5507200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:5506400-5507400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:5506400-5507400	Enhancers	Fetal Thymus	thymus
41	chr6:5506400-5508000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:5506600-5507400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:5506600-5507400	Enhancers	Primary hematopoietic stem cells	blood
44	chr6:5506600-5508000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:5506600-5512000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:5506800-5507200	Enhancers	Thymus	Thymus
47	chr6:5506800-5507400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr6:5506800-5507400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:5506800-5507600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:5506800-5507600	Enhancers	Osteobl	bone

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