Variant report

Variant	rs3799599
Chromosome Location	chr6:167001998-167001999
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	REST	chr6:167001166-167002860	HL-60	blood:	n/a	chr6:167002009-167002029
2	FOXM1	chr6:167001391-167002055	GM12878	blood:	n/a	n/a
3	REST	chr6:167001544-167002060	GM12878	blood:	n/a	chr6:167002009-167002029
4	RELA	chr6:167001189-167002864	GM10847	blood:	n/a	n/a
5	CHD1	chr6:167001924-167002124	GM12878	blood:	n/a	n/a
6	ELF1	chr6:167001967-167002513	GM12878	blood:	n/a	chr6:167002240-167002249
7	SPI1	chr6:167001170-167002630	GM12878	blood:	n/a	chr6:167001694-167001707
8	POLR2A	chr6:167000381-167003269	GM12891	blood:	n/a	n/a
9	REST	chr6:167001179-167002028	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:167000300-167002507	Raji	blood:	n/a	n/a
11	STAT5A	chr6:167001552-167002019	GM12878	blood:	n/a	n/a
12	RELA	chr6:167001136-167002056	GM18951	blood:	n/a	n/a
13	RELA	chr6:167001175-167003175	GM18505	blood:	n/a	n/a
14	RELA	chr6:167000797-167003486	GM12891	blood:	n/a	n/a
15	RELA	chr6:167001203-167002781	GM19193	blood:	n/a	n/a
16	ELF1	chr6:167001090-167002015	GM12878	blood:	n/a	n/a
17	MTA3	chr6:167000979-167002760	GM12878	blood:	n/a	n/a
18	REST	chr6:167001482-167002135	HL-60	blood:	n/a	chr6:167002009-167002029

Variant related genes	Relation type
FAM103A2P	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12528284	0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12661452	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2032544	0.89[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2032545	0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34324183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35574615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35798186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799579	0.90[CHB][hapmap]
rs3799581	0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs3799582	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3799589	0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3799590	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799591	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799592	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799593	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799594	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3799595	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3799596	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799616	0.82[JPT][hapmap]
rs3823196	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823197	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3823198	0.89[CHB][hapmap];0.91[ASN][1000 genomes]
rs3823204	0.82[JPT][hapmap]
rs6907098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6907443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs733591	0.83[ASN][1000 genomes]
rs763193	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs9295356	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9347138	0.90[CHB][hapmap]
rs9348149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9355586	0.87[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9356491	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9356493	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9356494	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9366029	0.81[ASN][1000 genomes]
rs9366031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366033	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs960145	0.89[CHB][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv5592	chr6:166958317-167002951	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
5	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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166981800-167002400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:166986200-167002200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:166986800-167003000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:166987000-167002000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:166989000-167011400	Weak transcription	Ovary	ovary
6	chr6:166993600-167003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:166994000-167003600	Weak transcription	Brain Germinal Matrix	brain
8	chr6:166994800-167002000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:166995600-167002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:166995800-167002200	Weak transcription	Right Ventricle	heart
12	chr6:166997000-167002200	Weak transcription	Pancreas	Pancrea
13	chr6:166997000-167003000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:166997200-167002000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:166997200-167002200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:166997200-167003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
18	chr6:166997400-167003000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:166997600-167002200	Weak transcription	HMEC	breast
20	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:166998200-167002200	Weak transcription	Left Ventricle	heart
22	chr6:166998600-167002400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:166998800-167002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:166998800-167002200	Weak transcription	NHLF	lung
25	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
26	chr6:166999000-167002000	Weak transcription	Osteobl	bone
27	chr6:166999000-167002200	Weak transcription	NHDF-Ad	bronchial
28	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
29	chr6:167000000-167003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr6:167000000-167003400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:167000200-167003600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
34	chr6:167000400-167002200	Weak transcription	Psoas Muscle	Psoas
35	chr6:167000400-167003000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:167000400-167004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:167000400-167004200	Enhancers	Fetal Muscle Leg	muscle
38	chr6:167000400-167004200	Enhancers	Spleen	Spleen
39	chr6:167000600-167003200	Enhancers	Primary T cells from cord blood	blood
40	chr6:167000600-167003400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:167000600-167003400	Flanking Active TSS	GM12878-XiMat	blood
42	chr6:167000600-167003800	Enhancers	Fetal Kidney	kidney
43	chr6:167000600-167004200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr6:167000600-167004200	Enhancers	HUVEC	blood vessel
45	chr6:167000600-167004400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr6:167000600-167004600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:167000800-167004000	Enhancers	Adipose Nuclei	Adipose
48	chr6:167000800-167004200	Enhancers	Primary hematopoietic stem cells	blood
49	chr6:167000800-167006200	Enhancers	Fetal Heart	heart
50	chr6:167001000-167002000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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