Variant report

Variant	rs1015139
Chromosome Location	chr6:5508618-5508619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17140739	0.94[CEU][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72817757	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72817759	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs765819	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9328306	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9378958	1.00[YRI][hapmap]
rs9502309	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9504417	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9504419	0.95[YRI][hapmap]
rs9504421	0.94[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1015139	PSMG4	cis	cerebellum	SCAN
rs1015139	CDYL	cis	cerebellum	SCAN
rs1015139	RIPK1	cis	cerebellum	SCAN
rs1015139	SLC22A23	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5466400-5518200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:5472400-5511600	Weak transcription	Fetal Stomach	stomach
3	chr6:5488000-5510600	Weak transcription	Aorta	Aorta
4	chr6:5488600-5521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr6:5498800-5513000	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:5500000-5510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:5500200-5511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr6:5500400-5510600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:5500400-5511800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:5500400-5525000	Weak transcription	Spleen	Spleen
11	chr6:5500600-5510600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:5500800-5511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:5501000-5511800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:5501000-5550600	Weak transcription	Pancreas	Pancrea
15	chr6:5501200-5511800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:5501400-5513400	Weak transcription	Brain Anterior Caudate	brain
17	chr6:5501600-5509000	Weak transcription	Right Ventricle	heart
18	chr6:5502400-5511200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:5502400-5511200	Weak transcription	Gastric	stomach
20	chr6:5503200-5510600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:5505800-5509000	Enhancers	Primary B cells from peripheral blood	blood
22	chr6:5506200-5509000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr6:5506600-5512000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:5507000-5508800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:5507000-5510400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:5507000-5510600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:5507200-5510400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr6:5507400-5510600	Enhancers	Fetal Heart	heart
29	chr6:5507600-5511600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:5507600-5511600	Weak transcription	Osteobl	bone
31	chr6:5507600-5512400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:5507800-5508800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:5507800-5509000	Enhancers	Fetal Thymus	thymus
34	chr6:5508000-5509000	Enhancers	Primary B cells from cord blood	blood
35	chr6:5508000-5509000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:5508000-5510600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:5508000-5511800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:5508000-5547400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:5508200-5509200	Weak transcription	Fetal Intestine Small	intestine
40	chr6:5508200-5510000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:5508200-5511000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:5508200-5511200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:5508200-5512000	Weak transcription	Thymus	Thymus
44	chr6:5508200-5512400	Weak transcription	Fetal Brain Male	brain
45	chr6:5508200-5516800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:5508200-5519400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:5508400-5509000	Enhancers	GM12878-XiMat	blood
48	chr6:5508400-5509400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:5508400-5516400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:5508600-5508800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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