Variant report

Variant	rs3799603
Chromosome Location	chr6:167001286-167001287
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	TCF3	chr6:167001167-167001431	GM12878	blood:	n/a	n/a
2	REST	chr6:167001166-167002860	HL-60	blood:	n/a	chr6:167002009-167002029
3	RUNX3	chr6:167001099-167001936	GM12878	blood:	n/a	n/a
4	TCF12	chr6:167001176-167001458	GM12878	blood:	n/a	n/a
5	RELA	chr6:167001189-167002864	GM10847	blood:	n/a	n/a
6	PBX3	chr6:167001171-167001413	GM12878	blood:	n/a	n/a
7	MAZ	chr6:167001188-167001858	GM12878	blood:	n/a	chr6:167001220-167001229
8	SPI1	chr6:167001170-167002630	GM12878	blood:	n/a	chr6:167001694-167001707
9	ELK1	chr6:167001257-167001842	GM12878	blood:	n/a	n/a
10	ELF1	chr6:167001137-167001439	GM12878	blood:	n/a	n/a
11	STAT3	chr6:167001272-167001846	GM12878	blood:	n/a	chr6:167001298-167001305
12	POLR2A	chr6:167000381-167003269	GM12891	blood:	n/a	n/a
13	REST	chr6:167001179-167002028	GM12878	blood:	n/a	n/a
14	PAX5	chr6:167001175-167001387	GM12878	blood:	n/a	n/a
15	YY1	chr6:167001175-167001443	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:167000300-167002507	Raji	blood:	n/a	n/a
17	RELA	chr6:167001136-167002056	GM18951	blood:	n/a	n/a
18	STAT1	chr6:167001257-167001802	GM12878	blood:	n/a	chr6:167001298-167001305
19	NFIC	chr6:167001123-167001910	GM12878	blood:	n/a	n/a
20	RUNX3	chr6:167001089-167001958	GM12878	blood:	n/a	n/a
21	BCLAF1	chr6:167001220-167001927	GM12878	blood:	n/a	n/a
22	RELA	chr6:167001175-167003175	GM18505	blood:	n/a	n/a
23	RELA	chr6:167000797-167003486	GM12891	blood:	n/a	n/a
24	RELA	chr6:167001203-167002781	GM19193	blood:	n/a	n/a
25	ELF1	chr6:167001090-167002015	GM12878	blood:	n/a	n/a
26	NFIC	chr6:167001143-167001959	GM12878	blood:	n/a	n/a
27	MTA3	chr6:167000979-167002760	GM12878	blood:	n/a	n/a
28	EBF1	chr6:167001178-167001440	GM12878	blood:	n/a	n/a
29	RCOR1	chr6:167001216-167001903	GM12878	blood:	n/a	n/a

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:19)

rs_ID	r²[population]
rs10214670	0.87[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs12190451	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778382	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778384	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778385	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3778386	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]
rs3799584	0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs3799597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[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];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4710069	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs4710070	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs4710071	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6928849	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7742514	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295353	0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs9457187	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9457189	0.83[CHB][hapmap]

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:81 , 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	chr6:166986600-167001400	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:166986800-167003000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:166987000-167002000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:166987200-167001800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:166989000-167011400	Weak transcription	Ovary	ovary
8	chr6:166989600-167001800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:166990600-167001800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:166993600-167003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:166993800-167001800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:166994000-167003600	Weak transcription	Brain Germinal Matrix	brain
13	chr6:166994800-167002000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:166995600-167002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:166995800-167001600	Weak transcription	Gastric	stomach
17	chr6:166995800-167002200	Weak transcription	Right Ventricle	heart
18	chr6:166996800-167001400	Weak transcription	Brain Anterior Caudate	brain
19	chr6:166997000-167002200	Weak transcription	Pancreas	Pancrea
20	chr6:166997000-167003000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:166997200-167002000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:166997200-167002200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:166997200-167003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
25	chr6:166997400-167003000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:166997600-167002200	Weak transcription	HMEC	breast
27	chr6:166997800-167001600	Weak transcription	Lung	lung
28	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:166998200-167002200	Weak transcription	Left Ventricle	heart
30	chr6:166998600-167001400	Weak transcription	Fetal Stomach	stomach
31	chr6:166998600-167002400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:166998800-167001400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:166998800-167001800	Weak transcription	Right Atrium	heart
34	chr6:166998800-167001800	Weak transcription	HSMMtube	muscle
35	chr6:166998800-167002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr6:166998800-167002200	Weak transcription	NHLF	lung
37	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
38	chr6:166999000-167001600	Weak transcription	HSMM	muscle
39	chr6:166999000-167002000	Weak transcription	Osteobl	bone
40	chr6:166999000-167002200	Weak transcription	NHDF-Ad	bronchial
41	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
42	chr6:167000000-167003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr6:167000000-167003400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:167000200-167001400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:167000200-167003600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
48	chr6:167000400-167001400	Enhancers	Primary B cells from cord blood	blood
49	chr6:167000400-167002200	Weak transcription	Psoas Muscle	Psoas
50	chr6:167000400-167003000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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