Variant report

Variant	rs3778386
Chromosome Location	chr6:167003338-167003339
allele	C/T
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	RELA	chr6:167000797-167003486	GM12891	blood:	n/a	n/a
2	KAP1	chr6:167003004-167004325	HEK293	kidney:	n/a	n/a
3	GATA3	chr6:167003327-167004080	SK-N-SH	brain:	n/a	chr6:167003791-167003807 chr6:167003794-167003804 chr6:167003794-167003803 chr6:167003791-167003807

Variant related genes	Relation type
FAM103A2P	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10214670	0.86[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs10946177	0.83[MEX][hapmap]
rs12190451	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778382	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778384	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778385	0.93[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799584	0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs3799597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799602	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4710069	0.83[CHB][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap]
rs4710070	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4710071	0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928849	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7742514	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295353	0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs9457187	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9457189	0.82[CHB][hapmap]

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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3778386	PDE10A	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166989000-167011400	Weak transcription	Ovary	ovary
2	chr6:166994000-167003600	Weak transcription	Brain Germinal Matrix	brain
3	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:166997200-167003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
6	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
8	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
9	chr6:167000000-167003400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:167000200-167003600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:167000400-167004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:167000400-167004200	Enhancers	Fetal Muscle Leg	muscle
15	chr6:167000400-167004200	Enhancers	Spleen	Spleen
16	chr6:167000600-167003400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:167000600-167003400	Flanking Active TSS	GM12878-XiMat	blood
18	chr6:167000600-167003800	Enhancers	Fetal Kidney	kidney
19	chr6:167000600-167004200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:167000600-167004200	Enhancers	HUVEC	blood vessel
21	chr6:167000600-167004400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:167000600-167004600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:167000800-167004000	Enhancers	Adipose Nuclei	Adipose
24	chr6:167000800-167004200	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:167000800-167006200	Enhancers	Fetal Heart	heart
26	chr6:167001200-167003600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:167001200-167004800	Enhancers	Fetal Muscle Trunk	muscle
28	chr6:167001400-167004000	Enhancers	Brain Hippocampus Middle	brain
29	chr6:167001400-167004000	Enhancers	Fetal Stomach	stomach
30	chr6:167001400-167004800	Enhancers	Brain Anterior Caudate	brain
31	chr6:167001600-167004000	Enhancers	HSMM	muscle
32	chr6:167001600-167004400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:167001800-167003400	Enhancers	Dnd41	blood
34	chr6:167001800-167003600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:167001800-167003600	Enhancers	Placenta	Placenta
36	chr6:167001800-167004200	Enhancers	Brain Substantia Nigra	brain
37	chr6:167001800-167004200	Enhancers	NH-A	brain
38	chr6:167001800-167004400	Enhancers	Brain Angular Gyrus	brain
39	chr6:167001800-167004600	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr6:167001800-167004600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:167001800-167005000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr6:167001800-167005400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:167002000-167003400	Enhancers	Colon Smooth Muscle	Colon
44	chr6:167002000-167003800	Enhancers	Duodenum Mucosa	Duodenum
45	chr6:167002000-167004200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:167002000-167004200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:167002000-167004200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:167002200-167003400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:167002200-167003600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:167002200-167003600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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