Variant report

Variant	rs12203960
Chromosome Location	chr6:161599406-161599407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10455875	1.00[ASN][1000 genomes]
rs11965825	1.00[CHD][hapmap]
rs12190406	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191615	1.00[CHD][hapmap]
rs12195072	1.00[CHD][hapmap]
rs12199314	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12203149	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204872	0.91[CEU][hapmap]
rs12208953	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524665	0.91[CEU][hapmap]
rs13196735	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197494	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212549	0.83[CEU][hapmap]
rs1474915	1.00[ASN][1000 genomes]
rs2064719	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277092	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34025755	1.00[ASN][1000 genomes]
rs6900500	1.00[CHD][hapmap]
rs6901905	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];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	1.00[ASN][1000 genomes]
rs7748827	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]

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	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	nsv949397	chr6:161592100-161812932	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv2752091	chr6:161592100-161855785	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12203960	AGPAT4	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161585600-161626000	Weak transcription	Right Atrium	heart
2	chr6:161587400-161599600	Weak transcription	Spleen	Spleen
3	chr6:161587400-161607000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:161588000-161599800	Weak transcription	Primary T cells from cord blood	blood
5	chr6:161590000-161611600	Weak transcription	HSMMtube	muscle
6	chr6:161590200-161607600	Weak transcription	HSMM	muscle
7	chr6:161590400-161606800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:161591000-161607000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:161591400-161626200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:161591600-161615400	Weak transcription	Fetal Heart	heart
11	chr6:161591800-161607000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:161592000-161599800	Weak transcription	Ovary	ovary
13	chr6:161592000-161607000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:161592000-161609600	Weak transcription	Fetal Brain Male	brain
15	chr6:161592200-161602200	Weak transcription	Brain Anterior Caudate	brain
16	chr6:161592200-161606600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:161593600-161599600	Weak transcription	Esophagus	oesophagus
18	chr6:161598400-161601400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:161598400-161602000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
20	chr6:161598400-161602200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:161598600-161601600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:161598600-161602400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
23	chr6:161598600-161602600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
24	chr6:161598800-161600400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:161598800-161600800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
26	chr6:161598800-161601400	ZNF genes & repeats	Lung	lung
27	chr6:161598800-161602400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:161599000-161600600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:161599000-161601400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:161599000-161601800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
31	chr6:161599000-161601800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:161599200-161599800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:161599200-161599800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr6:161599200-161599800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
35	chr6:161599200-161600600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
36	chr6:161599200-161600800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:161599200-161601400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:161599200-161601400	ZNF genes & repeats	Fetal Muscle Leg	muscle
39	chr6:161599400-161600000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:161599400-161600600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
41	chr6:161599400-161601200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr6:161599400-161606800	Weak transcription	Osteobl	bone

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