Variant report

Variant	rs9504399
Chromosome Location	chr6:5460612-5460613
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5455034..5457596-chr6:5459159..5460952,3	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17140504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17140536	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.90[ASN][1000 genomes]
rs17299552	0.90[ASN][1000 genomes]
rs58808190	0.90[ASN][1000 genomes]
rs6920599	1.00[MEX][hapmap]
rs9502304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9504401	0.95[ASN][1000 genomes]
rs9504403	0.91[ASN][1000 genomes]

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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5433600-5461400	Weak transcription	Fetal Stomach	stomach
2	chr6:5434200-5487000	Weak transcription	Aorta	Aorta
3	chr6:5437400-5471200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:5438200-5471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:5448600-5466800	Weak transcription	Primary B cells from cord blood	blood
6	chr6:5449000-5499400	Weak transcription	Fetal Intestine Large	intestine
7	chr6:5453000-5471000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:5454800-5472000	Weak transcription	Spleen	Spleen
9	chr6:5456400-5486000	Weak transcription	Thymus	Thymus
10	chr6:5457400-5481200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:5457600-5466400	Weak transcription	NHDF-Ad	bronchial
12	chr6:5457600-5472600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:5457800-5463200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:5457800-5471400	Weak transcription	Brain Substantia Nigra	brain
15	chr6:5457800-5487400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:5458200-5463000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:5458400-5460800	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:5458400-5461000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:5458400-5461400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:5458400-5464000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:5458400-5464000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:5458400-5464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:5458600-5461800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:5458600-5464200	Weak transcription	Right Atrium	heart
25	chr6:5458600-5466600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr6:5458600-5466800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:5458600-5466800	Weak transcription	Left Ventricle	heart
28	chr6:5458800-5464400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:5458800-5464400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:5458800-5464400	Weak transcription	Lung	lung
31	chr6:5458800-5466800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:5458800-5469400	Weak transcription	Esophagus	oesophagus
33	chr6:5458800-5471400	Weak transcription	Brain Angular Gyrus	brain
34	chr6:5458800-5483000	Weak transcription	Pancreas	Pancrea
35	chr6:5459000-5466400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:5459000-5486400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:5459200-5471200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:5459600-5469400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:5459800-5461400	Enhancers	Primary T cells from cord blood	blood
40	chr6:5459800-5466600	Weak transcription	Osteobl	bone
41	chr6:5460000-5461600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr6:5460000-5461800	Weak transcription	Fetal Brain Male	brain
43	chr6:5460000-5462600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:5460000-5463000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:5460000-5464000	Weak transcription	HSMM	muscle
46	chr6:5460000-5464400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:5460200-5461200	Enhancers	Primary hematopoietic stem cells	blood
48	chr6:5460200-5463000	Weak transcription	HSMMtube	muscle
49	chr6:5460200-5463200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr6:5460200-5466400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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