Variant report

Variant	rs3778384
Chromosome Location	chr6:167003720-167003721
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	KAP1	chr6:167003608-167004182	U2OS	brain:	n/a	n/a
2	KAP1	chr6:167003004-167004325	HEK293	kidney:	n/a	n/a
3	GATA2	chr6:167003399-167004068	SH-SY5Y	brain:	n/a	chr6:167003791-167003807 chr6:167003794-167003804 chr6:167003794-167003803 chr6:167003791-167003807
4	GATA3	chr6:167003327-167004080	SK-N-SH	brain:	n/a	chr6:167003791-167003807 chr6:167003794-167003804 chr6:167003794-167003803 chr6:167003791-167003807
5	GATA3	chr6:167003508-167004186	SH-SY5Y	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: 0)

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

rs_ID	r²[population]
rs10214670	0.91[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10946177	0.87[MEX][hapmap];0.82[EUR][1000 genomes]
rs12190451	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778382	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778385	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778386	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]
rs3799584	0.91[JPT][hapmap];0.86[TSI][hapmap]
rs3799597	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799598	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799600	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799602	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799603	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4710069	0.83[CHB][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap]
rs4710070	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4710071	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928849	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742514	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295353	0.91[JPT][hapmap]
rs9457187	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];1.00[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

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166989000-167011400	Weak transcription	Ovary	ovary
2	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
4	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
6	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
7	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:167000400-167004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:167000400-167004200	Enhancers	Fetal Muscle Leg	muscle
11	chr6:167000400-167004200	Enhancers	Spleen	Spleen
12	chr6:167000600-167003800	Enhancers	Fetal Kidney	kidney
13	chr6:167000600-167004200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:167000600-167004200	Enhancers	HUVEC	blood vessel
15	chr6:167000600-167004400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:167000600-167004600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:167000800-167004000	Enhancers	Adipose Nuclei	Adipose
18	chr6:167000800-167004200	Enhancers	Primary hematopoietic stem cells	blood
19	chr6:167000800-167006200	Enhancers	Fetal Heart	heart
20	chr6:167001200-167004800	Enhancers	Fetal Muscle Trunk	muscle
21	chr6:167001400-167004000	Enhancers	Brain Hippocampus Middle	brain
22	chr6:167001400-167004000	Enhancers	Fetal Stomach	stomach
23	chr6:167001400-167004800	Enhancers	Brain Anterior Caudate	brain
24	chr6:167001600-167004000	Enhancers	HSMM	muscle
25	chr6:167001600-167004400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:167001800-167004200	Enhancers	Brain Substantia Nigra	brain
27	chr6:167001800-167004200	Enhancers	NH-A	brain
28	chr6:167001800-167004400	Enhancers	Brain Angular Gyrus	brain
29	chr6:167001800-167004600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:167001800-167004600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr6:167001800-167005000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:167001800-167005400	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr6:167002000-167003800	Enhancers	Duodenum Mucosa	Duodenum
34	chr6:167002000-167004200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:167002000-167004200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:167002000-167004200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:167002200-167003800	Enhancers	NHLF	lung
38	chr6:167002200-167005200	Enhancers	Left Ventricle	heart
39	chr6:167002200-167005400	Enhancers	Right Ventricle	heart
40	chr6:167002200-167006600	Enhancers	Psoas Muscle	Psoas
41	chr6:167002400-167003800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:167002400-167003800	Enhancers	Rectal Smooth Muscle	rectum
43	chr6:167002400-167004800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:167002600-167003800	Weak transcription	Pancreas	Pancrea
45	chr6:167002600-167005400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:167002600-167011400	Weak transcription	Right Atrium	heart
47	chr6:167002600-167013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:167003000-167004000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:167003000-167004000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr6:167003000-167004200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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