Variant report

Variant	rs12528948
Chromosome Location	chr6:80724666-80724667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80724231..80726532-chr6:80730064..80732881,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12524041	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12524658	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527889	1.00[JPT][hapmap]
rs12528075	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12529133	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529575	1.00[JPT][hapmap]
rs12530290	1.00[JPT][hapmap]
rs1550035	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17174951	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17175251	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17176133	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17254389	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17254634	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801460	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801465	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823176	1.00[JPT][hapmap]
rs4547972	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs45495802	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4613770	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4642425	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55956173	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56219628	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56302322	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62405965	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62405967	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405994	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405995	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62405997	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62405999	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62406015	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62406016	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7765797	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769377	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv5370	chr6:80715351-80751740	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv886306	chr6:80724666-80754346	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv886307	chr6:80724666-80765111	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12528948	PGM3	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80714800-80738800	Weak transcription	Small Intestine	intestine
2	chr6:80715000-80730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:80715000-80748000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:80715000-80752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:80715000-80752400	Weak transcription	Placenta	Placenta
6	chr6:80715200-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:80715200-80727000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:80715200-80730800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:80715200-80734000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:80715200-80734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:80715200-80739200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:80715200-80749600	Weak transcription	Fetal Intestine Small	intestine
13	chr6:80715200-80752000	Weak transcription	Primary B cells from cord blood	blood
14	chr6:80715200-80752200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:80715400-80726000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:80715400-80727000	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:80715400-80729400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr6:80715400-80742200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:80715400-80743200	Weak transcription	Brain Germinal Matrix	brain
20	chr6:80715400-80745400	Weak transcription	Fetal Lung	lung
21	chr6:80715400-80755000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:80715400-80756800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:80715600-80725200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:80715600-80739200	Weak transcription	Fetal Stomach	stomach
25	chr6:80715600-80754400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:80715600-80763800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:80715800-80733400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:80715800-80753600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:80715800-80753800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:80715800-80754400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:80716000-80726000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:80716000-80728600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:80716000-80729400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:80716000-80739200	Weak transcription	NHEK	skin
35	chr6:80716000-80743600	Weak transcription	Fetal Heart	heart
36	chr6:80716200-80725200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:80716200-80727800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:80716200-80728000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:80716200-80754600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr6:80716400-80727800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:80716800-80753600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr6:80717000-80728000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:80717400-80724800	Strong transcription	NH-A	brain
44	chr6:80717400-80727400	Strong transcription	HUVEC	blood vessel
45	chr6:80717400-80728000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr6:80717400-80739200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr6:80717600-80726800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:80717600-80727800	Strong transcription	HSMM	muscle
49	chr6:80718000-80728000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:80718000-80728000	Strong transcription	Fetal Thymus	thymus

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