Variant report

Variant	rs8109914
Chromosome Location	chr19:39517062-39517063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr19:39516890-39517218	GM12878	blood:	n/a	chr19:39517075-39517086

Variant related genes	Relation type
ENSG00000267992	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10410965	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11666514	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12150941	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1268240	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs1268251	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12978285	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2081994	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2081995	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2318895	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2318896	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2873834	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2873835	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2873836	0.91[ASN][1000 genomes]
rs34640039	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4305198	0.91[EUR][1000 genomes]
rs472104	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[ASN][1000 genomes]
rs473729	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs473878	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[ASN][1000 genomes]
rs476616	0.81[ASN][1000 genomes]
rs479001	0.90[ASN][1000 genomes]
rs4802004	0.91[ASN][1000 genomes]
rs4802012	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803179	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4803180	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803184	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485226	0.89[ASN][1000 genomes]
rs497378	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs533573	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536244	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs580494	0.89[ASN][1000 genomes]
rs601966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs603268	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs631879	0.81[ASN][1000 genomes]
rs631952	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs646580	0.89[ASN][1000 genomes]
rs650450	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7247817	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7254745	0.83[ASN][1000 genomes]
rs7258182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73047946	0.81[ASN][1000 genomes]
rs8105050	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8109914	LOC390940	cis	cerebellum	SCAN
rs8109914	BLOC1S3	cis	cerebellum	SCAN
rs8109914	PSG3	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39487200-39518200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:39502400-39518000	Weak transcription	Aorta	Aorta
3	chr19:39503600-39520200	Weak transcription	Liver	Liver
4	chr19:39506800-39517200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:39507200-39517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:39511200-39517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:39512400-39518000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:39513000-39521600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:39513000-39521600	Weak transcription	Right Atrium	heart
10	chr19:39513200-39517400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr19:39513600-39517400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr19:39514000-39517600	Weak transcription	NHEK	skin
13	chr19:39514000-39521400	Weak transcription	Pancreas	Pancrea
14	chr19:39514000-39522200	Weak transcription	Gastric	stomach
15	chr19:39514200-39517800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:39514200-39517800	Weak transcription	Placenta	Placenta
17	chr19:39514400-39517400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr19:39514400-39517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:39514400-39517800	Weak transcription	Brain Germinal Matrix	brain
20	chr19:39514400-39517800	Weak transcription	Left Ventricle	heart
21	chr19:39514400-39520400	Weak transcription	Fetal Intestine Large	intestine
22	chr19:39514400-39521600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:39514400-39521800	Weak transcription	Colon Smooth Muscle	Colon
24	chr19:39514600-39517600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:39514600-39517600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr19:39514600-39521400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:39514800-39517600	Weak transcription	Lung	lung
28	chr19:39514800-39518600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:39514800-39519600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:39514800-39520000	Strong transcription	Brain Cingulate Gyrus	brain
31	chr19:39515000-39517200	Enhancers	GM12878-XiMat	blood
32	chr19:39515000-39518000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:39515200-39521600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr19:39515400-39517400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:39515400-39519000	Strong transcription	Brain Hippocampus Middle	brain
36	chr19:39515600-39517800	Strong transcription	Fetal Stomach	stomach
37	chr19:39515600-39518400	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr19:39515600-39518600	Strong transcription	Brain Substantia Nigra	brain
39	chr19:39515600-39518800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:39515800-39517600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:39515800-39518000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr19:39515800-39518400	Strong transcription	Adipose Nuclei	Adipose
43	chr19:39515800-39518600	Strong transcription	Ovary	ovary
44	chr19:39516000-39517600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr19:39516000-39518200	Strong transcription	Brain Angular Gyrus	brain
46	chr19:39516200-39521000	Weak transcription	K562	blood
47	chr19:39516200-39521600	Weak transcription	Right Ventricle	heart
48	chr19:39516400-39518000	Weak transcription	Fetal Heart	heart
49	chr19:39516400-39522200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:39516600-39518400	ZNF genes & repeats	A549	lung

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