Variant report

Variant	rs2299049
Chromosome Location	chr6:15434412-15434413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15424021..15426137-chr6:15433751..15436727,2	K562	blood:
2	chr6:15432414..15437643-chr6:15439715..15443191,6	K562	blood:
3	chr6:15428361..15431112-chr6:15432614..15434598,3	K562	blood:
4	chr6:14883074..14885637-chr6:15431868..15434468,2	K562	blood:
5	chr6:15364856..15367821-chr6:15434110..15436530,2	K562	blood:
6	chr6:15433530..15436747-chr6:15439990..15443191,3	K562	blood:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13193457	0.93[JPT][hapmap]
rs16876291	0.93[JPT][hapmap]
rs2237142	0.84[MEX][hapmap]
rs2299047	0.94[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35434217	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35536104	0.84[ASN][1000 genomes]
rs4712251	0.83[CHB][hapmap]
rs6935676	0.86[JPT][hapmap]
rs7753636	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299049	HIVEP1	cis	cerebellum	SCAN
rs2299049	SIRT5	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15417000-15452200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr6:15424600-15442000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr6:15425600-15445400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:15425800-15437800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:15426000-15435000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:15426000-15441000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:15426400-15440400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:15426400-15442000	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:15426800-15434800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:15427000-15450800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:15428000-15435200	Enhancers	Brain Hippocampus Middle	brain
12	chr6:15428000-15441800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr6:15428400-15436600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:15428400-15437400	Weak transcription	Dnd41	blood
15	chr6:15428800-15441600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr6:15429000-15435000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:15429000-15435000	Enhancers	Brain Substantia Nigra	brain
18	chr6:15429200-15446000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:15429400-15435800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:15430000-15434800	Enhancers	Adipose Nuclei	Adipose
21	chr6:15430000-15434800	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr6:15430200-15435000	Enhancers	HSMM	muscle
23	chr6:15430200-15439600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr6:15430200-15439600	Weak transcription	NHLF	lung
25	chr6:15430800-15435000	Enhancers	Small Intestine	intestine
26	chr6:15430800-15440800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:15430800-15441000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr6:15430800-15441600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr6:15431000-15441600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:15431200-15435200	Enhancers	K562	blood
31	chr6:15431400-15434800	Enhancers	Fetal Thymus	thymus
32	chr6:15431400-15435000	Enhancers	Rectal Smooth Muscle	rectum
33	chr6:15431600-15434800	Enhancers	Placenta	Placenta
34	chr6:15431600-15435400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:15431800-15435000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:15431800-15435000	Enhancers	HMEC	breast
37	chr6:15431800-15435400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:15431800-15441600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr6:15432000-15435400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:15432000-15436600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:15432000-15436800	Enhancers	NHEK	skin
42	chr6:15432200-15434800	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:15432200-15434800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:15432400-15435800	Enhancers	HepG2	liver
45	chr6:15432400-15437200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:15432400-15439000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr6:15432400-15441600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:15432600-15435600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr6:15432600-15435600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:15432800-15434800	Enhancers	Brain Anterior Caudate	brain

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