Variant report

Variant	rs12546520
Chromosome Location	chr8:103832256-103832257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103831069..103833953-chr8:103874895..103877224,2	K562	blood:
2	chr8:103830021..103831891-chr8:103831974..103834449,2	K562	blood:
3	chr8:103665222..103669765-chr8:103830121..103834964,5	MCF-7	breast:
4	chr8:103819401..103822063-chr8:103831348..103833645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155096	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000253320	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11986658	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11989703	0.93[EUR][1000 genomes]
rs12545210	0.88[EUR][1000 genomes]
rs13123	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs2304344	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304348	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs4734672	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs4734677	0.84[EUR][1000 genomes]
rs62522580	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62526531	0.89[EUR][1000 genomes]
rs6985891	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs72686911	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7826791	0.88[EUR][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	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv465751	chr8:103817106-103894326	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv611822	chr8:103817106-103894326	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12546520	PCGF2	trans	parietal	SCAN
rs12546520	AZIN1	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103822800-103837400	Weak transcription	Gastric	stomach
2	chr8:103823000-103835600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr8:103823000-103835600	Weak transcription	Adipose Nuclei	Adipose
4	chr8:103823000-103837200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:103823000-103839600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr8:103823000-103841400	Weak transcription	Pancreas	Pancrea
7	chr8:103823000-103855000	Weak transcription	Esophagus	oesophagus
8	chr8:103823200-103841800	Weak transcription	Aorta	Aorta
9	chr8:103823200-103844000	Weak transcription	Right Ventricle	heart
10	chr8:103823200-103853400	Weak transcription	Right Atrium	heart
11	chr8:103823400-103870600	Weak transcription	Stomach Mucosa	stomach
12	chr8:103823600-103834800	Weak transcription	Fetal Brain Female	brain
13	chr8:103823600-103837400	Weak transcription	Brain Hippocampus Middle	brain
14	chr8:103823600-103838800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr8:103823600-103839800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr8:103823600-103840000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr8:103823800-103837600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:103823800-103837800	Weak transcription	NHDF-Ad	bronchial
19	chr8:103824000-103835000	Weak transcription	HSMMtube	muscle
20	chr8:103824000-103835000	Weak transcription	NHEK	skin
21	chr8:103824000-103835200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:103824000-103835200	Weak transcription	NHLF	lung
23	chr8:103824200-103835000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:103824200-103836600	Weak transcription	Fetal Intestine Large	intestine
25	chr8:103825600-103837600	Weak transcription	Dnd41	blood
26	chr8:103825600-103841600	Weak transcription	Lung	lung
27	chr8:103825800-103834600	Weak transcription	Osteobl	bone
28	chr8:103825800-103835000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr8:103825800-103836000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr8:103825800-103836200	Weak transcription	HMEC	breast
31	chr8:103825800-103837200	Weak transcription	Spleen	Spleen
32	chr8:103825800-103840200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr8:103826200-103839200	Weak transcription	HUVEC	blood vessel
34	chr8:103826800-103837400	Weak transcription	Colonic Mucosa	Colon
35	chr8:103826800-103837600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr8:103826800-103841400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr8:103826800-103871200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr8:103827000-103832600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr8:103827000-103833000	Weak transcription	A549	lung
40	chr8:103827000-103833400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr8:103827000-103833600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr8:103827000-103835000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr8:103827000-103835200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr8:103827000-103835600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr8:103827000-103835600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr8:103827000-103835800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr8:103827000-103835800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr8:103827000-103836000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr8:103827000-103838000	Weak transcription	Hela-S3	cervix
50	chr8:103827000-103838800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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