Variant report

Variant	rs3799598
Chromosome Location	chr6:167002252-167002253
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	TEAD4	chr6:167002245-167003207	ECC-1	luminal epithelium:	n/a	n/a
2	REST	chr6:167001166-167002860	HL-60	blood:	n/a	chr6:167002009-167002029
3	PBX3	chr6:167002103-167002416	GM12878	blood:	n/a	n/a
4	YY1	chr6:167002147-167002528	ECC-1	luminal epithelium:	n/a	n/a
5	TBL1XR1	chr6:167002074-167003079	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:167002172-167002532	ECC-1	luminal epithelium:	n/a	n/a
7	RELA	chr6:167002216-167003151	GM19099	blood:	n/a	n/a
8	TCF12	chr6:167002193-167003136	SK-N-SH	brain:	n/a	chr6:167002764-167002772
9	TAF1	chr6:167002066-167002532	ECC-1	luminal epithelium:	n/a	n/a
10	RELA	chr6:167001189-167002864	GM10847	blood:	n/a	n/a
11	ELF1	chr6:167002090-167002407	HepG2	liver:	n/a	chr6:167002240-167002249
12	PAX5	chr6:167002230-167002756	GM12878	blood:	n/a	n/a
13	ELF1	chr6:167001967-167002513	GM12878	blood:	n/a	chr6:167002240-167002249
14	SPI1	chr6:167001170-167002630	GM12878	blood:	n/a	chr6:167001694-167001707
15	ZEB1	chr6:167002096-167002549	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:167000381-167003269	GM12891	blood:	n/a	n/a
17	RCOR1	chr6:167002175-167002259	GM12878	blood:	n/a	n/a
18	CTCF	chr6:167002220-167002370	GM12873	blood:	n/a	n/a
19	FOXM1	chr6:167002143-167002794	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:167000300-167002507	Raji	blood:	n/a	n/a
21	POLR2A	chr6:167002181-167002486	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr6:167002055-167002913	ECC-1	luminal epithelium:	n/a	chr6:167002532-167002541
23	TEAD4	chr6:167002250-167003032	ECC-1	luminal epithelium:	n/a	n/a
24	EBF1	chr6:167002248-167002687	GM12878	blood:	n/a	n/a
25	MAX	chr6:167002247-167002782	NB4	blood:	n/a	chr6:167002532-167002541
26	RFX5	chr6:167002126-167002459	GM12878	blood:	n/a	n/a
27	ZEB1	chr6:167002219-167002544	GM12878	blood:	n/a	n/a
28	RELA	chr6:167001175-167003175	GM18505	blood:	n/a	n/a
29	MAX	chr6:167002047-167002557	ECC-1	luminal epithelium:	n/a	chr6:167002532-167002541
30	RELA	chr6:167000797-167003486	GM12891	blood:	n/a	n/a
31	RELA	chr6:167001203-167002781	GM19193	blood:	n/a	n/a
32	CHD2	chr6:167002247-167002564	GM12878	blood:	n/a	chr6:167002440-167002450
33	MTA3	chr6:167000979-167002760	GM12878	blood:	n/a	n/a
34	NFYB	chr6:167002169-167002518	GM12878	blood:	n/a	n/a
35	MEF2A	chr6:167002178-167002772	GM12878	blood:	n/a	chr6:167002533-167002541
36	PBX3	chr6:167002163-167002361	GM12878	blood:	n/a	n/a
37	POU2F2	chr6:167002163-167002576	GM12891	blood:	n/a	n/a
38	PBX3	chr6:167002047-167003051	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
FAM103A2P	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10214670	0.86[CEU][hapmap];0.82[CHB][hapmap];0.86[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];0.99[ASN][1000 genomes]
rs3778382	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778384	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778385	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[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];0.99[ASN][1000 genomes]
rs3799584	0.81[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs3799597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799600	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];1.00[ASN][1000 genomes]
rs3799602	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799603	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]
rs4710069	0.80[CEU][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap]
rs4710070	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4710071	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928849	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742514	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295353	0.81[CEU][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs9295355	0.81[CHB][hapmap]
rs9457187	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9457189	0.86[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:92 , 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	chr6:166986800-167003000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:166989000-167011400	Weak transcription	Ovary	ovary
4	chr6:166993600-167003000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:166994000-167003600	Weak transcription	Brain Germinal Matrix	brain
6	chr6:166995000-167008400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:166995600-167002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:166997000-167003000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:166997200-167003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:166997200-167006000	Weak transcription	Aorta	Aorta
11	chr6:166997400-167003000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr6:166998600-167002400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:166998800-167004000	Weak transcription	Fetal Brain Male	brain
15	chr6:166999800-167004000	Enhancers	Fetal Thymus	thymus
16	chr6:167000000-167003000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:167000000-167003400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:167000000-167004400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:167000200-167003600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:167000200-167004600	Enhancers	Primary B cells from peripheral blood	blood
21	chr6:167000400-167003000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:167000400-167004000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:167000400-167004200	Enhancers	Fetal Muscle Leg	muscle
24	chr6:167000400-167004200	Enhancers	Spleen	Spleen
25	chr6:167000600-167003200	Enhancers	Primary T cells from cord blood	blood
26	chr6:167000600-167003400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:167000600-167003400	Flanking Active TSS	GM12878-XiMat	blood
28	chr6:167000600-167003800	Enhancers	Fetal Kidney	kidney
29	chr6:167000600-167004200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:167000600-167004200	Enhancers	HUVEC	blood vessel
31	chr6:167000600-167004400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:167000600-167004600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:167000800-167004000	Enhancers	Adipose Nuclei	Adipose
34	chr6:167000800-167004200	Enhancers	Primary hematopoietic stem cells	blood
35	chr6:167000800-167006200	Enhancers	Fetal Heart	heart
36	chr6:167001000-167002600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:167001200-167002600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr6:167001200-167003200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr6:167001200-167003600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr6:167001200-167004800	Enhancers	Fetal Muscle Trunk	muscle
41	chr6:167001400-167003200	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr6:167001400-167004000	Enhancers	Brain Hippocampus Middle	brain
43	chr6:167001400-167004000	Enhancers	Fetal Stomach	stomach
44	chr6:167001400-167004800	Enhancers	Brain Anterior Caudate	brain
45	chr6:167001600-167002400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:167001600-167002400	Enhancers	Gastric	stomach
47	chr6:167001600-167002600	Enhancers	Fetal Intestine Small	intestine
48	chr6:167001600-167002600	Enhancers	Lung	lung
49	chr6:167001600-167003000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr6:167001600-167004000	Enhancers	HSMM	muscle

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