Variant report

Variant	rs3778382
Chromosome Location	chr6:167004030-167004031
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: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10214670	0.90[EUR][1000 genomes]
rs10946177	0.82[EUR][1000 genomes]
rs12190451	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778384	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778385	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778386	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799597	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799598	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799600	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799602	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799603	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4710071	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928849	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742514	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457187	0.87[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	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:76 , 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	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:167000400-167004200	Enhancers	Fetal Muscle Leg	muscle
8	chr6:167000400-167004200	Enhancers	Spleen	Spleen
9	chr6:167000600-167004200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:167000600-167004200	Enhancers	HUVEC	blood vessel
11	chr6:167000600-167004400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr6:167000600-167004600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:167000800-167004200	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:167000800-167006200	Enhancers	Fetal Heart	heart
15	chr6:167001200-167004800	Enhancers	Fetal Muscle Trunk	muscle
16	chr6:167001400-167004800	Enhancers	Brain Anterior Caudate	brain
17	chr6:167001600-167004400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:167001800-167004200	Enhancers	Brain Substantia Nigra	brain
19	chr6:167001800-167004200	Enhancers	NH-A	brain
20	chr6:167001800-167004400	Enhancers	Brain Angular Gyrus	brain
21	chr6:167001800-167004600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr6:167001800-167004600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr6:167001800-167005000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:167001800-167005400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:167002000-167004200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:167002000-167004200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:167002000-167004200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:167002200-167005200	Enhancers	Left Ventricle	heart
29	chr6:167002200-167005400	Enhancers	Right Ventricle	heart
30	chr6:167002200-167006600	Enhancers	Psoas Muscle	Psoas
31	chr6:167002400-167004800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr6:167002600-167005400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:167002600-167011400	Weak transcription	Right Atrium	heart
34	chr6:167002600-167013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:167003000-167004200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:167003000-167009000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:167003000-167010400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:167003000-167010800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:167003200-167004200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:167003200-167004200	Enhancers	Osteobl	bone
41	chr6:167003200-167004800	Enhancers	Primary B cells from cord blood	blood
42	chr6:167003200-167004800	Enhancers	Esophagus	oesophagus
43	chr6:167003200-167006400	Weak transcription	Primary T cells from cord blood	blood
44	chr6:167003200-167009600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:167003200-167011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr6:167003200-167011200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:167003400-167004200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:167003400-167004600	Enhancers	GM12878-XiMat	blood
49	chr6:167003400-167005800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:167003400-167005800	Enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links