Variant report

Variant	rs2299027
Chromosome Location	chr6:13661270-13661271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13656757..13659128-chr6:13659241..13662282,5	K562	blood:
2	chr6:13651237..13655729-chr6:13659115..13661394,7	K562	blood:
3	chr6:13658437..13662774-chr6:13709974..13712662,5	K562	blood:
4	chr6:13658437..13687167-chr6:13707669..13717356,51	K562	blood:
5	chr6:13624060..13626610-chr6:13660365..13663120,2	MCF-7	breast:
6	chr6:13618139..13620523-chr6:13661080..13663050,2	K562	blood:
7	chr6:13647295..13649197-chr6:13661190..13662891,2	K562	blood:
8	chr6:13659651..13661542-chr6:13715805..13717920,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10484251	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948811	0.84[CHB][hapmap]
rs11753232	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11755634	0.84[CHB][hapmap]
rs11759518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573702	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs17213683	0.91[CHB][hapmap]
rs2071836	0.84[CHB][hapmap]
rs2253217	0.86[CEU][hapmap];0.87[GIH][hapmap]
rs2299026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752501	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757256	0.80[ASN][1000 genomes]
rs3846912	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs3906327	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs4715512	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs6459020	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs6459025	0.82[CHD][hapmap]
rs6911121	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs6935036	0.80[ASN][1000 genomes]
rs72831050	0.80[ASN][1000 genomes]
rs7744218	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs9475276	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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	74 gene(s)	inside rSNPs	diseases
2	nsv1016744	chr6:13622143-13664028	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1019422	chr6:13622143-13694781	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv1026597	chr6:13634669-13689882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2299027	RANBP9	cis	cerebellum	SCAN
rs2299027	SIRT5	cis	parietal	SCAN
rs2299027	SIRT5	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13620600-13691000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:13626600-13667800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:13626800-13669000	Weak transcription	Brain Anterior Caudate	brain
4	chr6:13638000-13661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:13639200-13662600	Weak transcription	Esophagus	oesophagus
6	chr6:13639400-13662000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:13639400-13666000	Weak transcription	Fetal Brain Female	brain
8	chr6:13639400-13667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:13639600-13662600	Weak transcription	Aorta	Aorta
10	chr6:13639800-13669800	Weak transcription	Fetal Intestine Small	intestine
11	chr6:13640000-13662600	Weak transcription	NHEK	skin
12	chr6:13640400-13662800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:13643800-13664400	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:13644000-13663600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:13645200-13666800	Weak transcription	HMEC	breast
16	chr6:13651400-13662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:13651600-13662200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:13652400-13662600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:13652400-13662800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:13652400-13665200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:13652400-13669600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:13652600-13667800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:13652600-13669800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:13653000-13662200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:13653000-13662800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:13653000-13663000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:13653000-13664200	Weak transcription	NHDF-Ad	bronchial
28	chr6:13653000-13674600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr6:13654600-13689800	Weak transcription	Osteobl	bone
30	chr6:13655200-13665800	Weak transcription	Fetal Thymus	thymus
31	chr6:13655400-13666800	Weak transcription	Stomach Mucosa	stomach
32	chr6:13655400-13677000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:13655600-13664000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr6:13657000-13680200	Weak transcription	HSMM	muscle
35	chr6:13657400-13666800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr6:13657600-13663600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:13657600-13663800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:13657600-13665600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:13657600-13666200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:13657600-13670400	Weak transcription	Dnd41	blood
41	chr6:13657800-13665000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:13658000-13666800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:13658200-13663800	Weak transcription	Primary B cells from cord blood	blood
44	chr6:13658800-13661600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:13658800-13670200	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr6:13659200-13661400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:13659200-13661400	Enhancers	Adipose Nuclei	Adipose
48	chr6:13659200-13670400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:13659400-13661600	Enhancers	Brain Angular Gyrus	brain
50	chr6:13659400-13661600	Enhancers	Fetal Heart	heart

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