Variant report

Variant	rs7748827
Chromosome Location	chr6:161588059-161588060
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:161574755..161576557-chr6:161587307..161589686,2	K562	blood:
2	chr6:161586766..161590077-chr6:161636291..161640021,3	K562	blood:
3	chr6:161586142..161588343-chr6:161615417..161617358,2	MCF-7	breast:
4	chr5:34856299..34858295-chr6:161586214..161589019,2	K562	blood:
5	chr6:161536783..161539702-chr6:161586448..161588143,2	K562	blood:
6	chr6:161585978..161588627-chr6:161656198..161658945,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10455875	1.00[ASN][1000 genomes]
rs11965825	1.00[CHD][hapmap];0.81[EUR][1000 genomes]
rs12190406	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191615	1.00[CHD][hapmap];0.83[EUR][1000 genomes]
rs12195072	0.85[CEU][hapmap];1.00[CHD][hapmap]
rs12199314	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12203149	1.00[ASN][1000 genomes]
rs12203960	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208953	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196735	1.00[ASN][1000 genomes]
rs13197494	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474915	1.00[ASN][1000 genomes]
rs16892225	0.81[EUR][1000 genomes]
rs2064719	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277092	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34025755	1.00[ASN][1000 genomes]
rs66683315	0.83[EUR][1000 genomes]
rs6900500	1.00[CHD][hapmap]
rs6901905	1.00[ASN][1000 genomes]
rs6902571	1.00[ASN][1000 genomes]
rs6923835	1.00[CHD][hapmap]
rs71565794	1.00[ASN][1000 genomes]
rs71565795	1.00[ASN][1000 genomes]
rs73786015	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886817	chr6:161371621-161846654	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3381361	chr6:161373617-161864101	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1030852	chr6:161477750-161589394	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7748827	AGPAT4	cis	cerebellum	SCAN
rs7748827	TMCC2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161544600-161589600	Weak transcription	Fetal Brain Male	brain
2	chr6:161548400-161590800	Weak transcription	Fetal Thymus	thymus
3	chr6:161549800-161589400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:161554000-161591000	Weak transcription	Colonic Mucosa	Colon
5	chr6:161558200-161589400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:161563400-161588200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:161574600-161592400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:161575600-161591000	Weak transcription	Gastric	stomach
9	chr6:161575600-161593400	Weak transcription	Esophagus	oesophagus
10	chr6:161579200-161590200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:161580600-161590800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:161582600-161591000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:161583600-161589200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:161583600-161589200	Weak transcription	HMEC	breast
15	chr6:161583600-161589200	Weak transcription	NHDF-Ad	bronchial
16	chr6:161583800-161590800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:161584000-161588200	Weak transcription	Pancreas	Pancrea
18	chr6:161584000-161589200	Weak transcription	Osteobl	bone
19	chr6:161584200-161589200	Weak transcription	HSMM	muscle
20	chr6:161584200-161589600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:161584200-161589600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr6:161584200-161589600	Weak transcription	HSMMtube	muscle
23	chr6:161584200-161591200	Weak transcription	Thymus	Thymus
24	chr6:161584200-161591800	Weak transcription	Right Ventricle	heart
25	chr6:161584600-161589000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:161584800-161589600	Weak transcription	Liver	Liver
27	chr6:161584800-161591200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:161585000-161589600	Weak transcription	Fetal Heart	heart
29	chr6:161585000-161591600	Weak transcription	Fetal Intestine Small	intestine
30	chr6:161585200-161589400	Weak transcription	Brain Angular Gyrus	brain
31	chr6:161585400-161588800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr6:161585400-161589200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:161585400-161589200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:161585600-161588800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:161585600-161589200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:161585600-161589200	Weak transcription	NHEK	skin
37	chr6:161585600-161589200	Weak transcription	NHLF	lung
38	chr6:161585600-161591200	Weak transcription	Ovary	ovary
39	chr6:161585600-161626000	Weak transcription	Right Atrium	heart
40	chr6:161585800-161589200	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:161586000-161588400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:161586400-161591000	Weak transcription	Fetal Kidney	kidney
43	chr6:161586600-161588400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:161586600-161589400	Weak transcription	Brain Anterior Caudate	brain
45	chr6:161586600-161590000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:161586600-161591000	Weak transcription	Lung	lung
47	chr6:161586800-161588800	Weak transcription	NH-A	brain
48	chr6:161586800-161589200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:161586800-161589200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:161586800-161589400	Weak transcription	Adipose Nuclei	Adipose

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