Variant report

Variant	rs3806284
Chromosome Location	chr1:181002479-181002480
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	MYC	chr1:181002070-181002666	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr1:181002382-181003223	IMR90	lung:	n/a	chr1:181002525-181002545 chr1:181003025-181003041 chr1:181002527-181002543 chr1:181002528-181002542
3	POLR2A	chr1:181002234-181003443	K562	blood:	n/a	n/a
4	MAFK	chr1:181002083-181003455	K562	blood:	n/a	chr1:181002525-181002545 chr1:181003025-181003041 chr1:181002527-181002543 chr1:181002528-181002542
5	EP300	chr1:181002369-181003339	GM12878	blood:	n/a	chr1:181002994-181003008 chr1:181002413-181002422 chr1:181003000-181003014
6	ELK1	chr1:181002306-181002537	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:181002338-181002494	Hela-S3	cervix:	n/a	n/a
8	MAX	chr1:181002270-181002707	GM12878	blood:	n/a	n/a
9	TBP	chr1:181002309-181003457	Hela-S3	cervix:	n/a	n/a
10	TBP	chr1:181002202-181003468	K562	blood:	n/a	n/a
11	EP300	chr1:181002289-181003517	K562	blood:	n/a	chr1:181002994-181003008 chr1:181002413-181002422 chr1:181003000-181003014
12	FOS	chr1:181002354-181002559	MCF10A-Er-Src	breast:	n/a	n/a
13	ELF1	chr1:181002222-181002549	GM12878	blood:	n/a	chr1:181002411-181002424 chr1:181002413-181002424
14	HCFC1	chr1:181002219-181002810	K562	blood:	n/a	n/a
15	POLR2A	chr1:181002227-181003490	Raji	blood:	n/a	n/a
16	POLR2A	chr1:181002325-181002543	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr1:181002278-181003453	K562	blood:	n/a	n/a
18	STAT3	chr1:181002293-181002659	MCF10A-Er-Src	breast:	n/a	n/a
19	YY1	chr1:181002233-181002593	GM12892	blood:	n/a	n/a
20	CHD2	chr1:181002236-181003370	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:181002207-181003384	MCF10A-Er-Src	breast:	n/a	n/a
22	USF2	chr1:181002248-181003414	Hela-S3	cervix:	n/a	n/a
23	BHLHE40	chr1:181001873-181003412	K562	blood:	n/a	n/a
24	POLR2A	chr1:181002263-181002527	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:181002079-181002749	GM12892	blood:	n/a	n/a
26	CEBPB	chr1:181002345-181002694	K562	blood:	n/a	n/a
27	E2F6	chr1:181002148-181002836	K562	blood:	n/a	n/a
28	MAX	chr1:181002226-181003447	Hela-S3	cervix:	n/a	chr1:181003414-181003424
29	RELA	chr1:181002244-181003519	GM19099	blood:	n/a	n/a
30	MAFK	chr1:181002427-181003436	Hela-S3	cervix:	n/a	chr1:181002525-181002545 chr1:181003025-181003041 chr1:181002527-181002543 chr1:181002528-181002542
31	SETDB1	chr1:181002265-181002742	U2OS	brain:	n/a	n/a
32	POLR2A	chr1:181002203-181003456	GM18505	blood:	n/a	n/a
33	POLR2A	chr1:181002056-181003460	GM12892	blood:	n/a	n/a
34	MAX	chr1:181002114-181002855	K562	blood:	n/a	n/a
35	CHD1	chr1:181002182-181003776	GM12878	blood:	n/a	n/a
36	MAX	chr1:181002191-181002751	K562	blood:	n/a	n/a
37	SPI1	chr1:181002056-181002851	GM12878	blood:	n/a	chr1:181002413-181002422 chr1:181002411-181002424 chr1:181002412-181002425 chr1:181002414-181002421
38	POLR2A	chr1:181002166-181002879	GM12891	blood:	n/a	n/a
39	MAX	chr1:181002089-181002877	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:181002278-181003349	GM15510	blood:	n/a	n/a
41	YY1	chr1:181002241-181002518	K562	blood:	n/a	n/a
42	MTA3	chr1:181002046-181003773	GM12878	blood:	n/a	n/a
43	CREB1	chr1:181002452-181003802	K562	blood:	n/a	n/a
44	CHD2	chr1:181001969-181003231	K562	blood:	n/a	n/a
45	UBTF	chr1:181002171-181002715	K562	blood:	n/a	n/a
46	YY1	chr1:181002204-181002628	GM12878	blood:	n/a	n/a
47	SPI1	chr1:181002236-181002567	K562	blood:	n/a	chr1:181002413-181002422 chr1:181002411-181002424 chr1:181002412-181002425 chr1:181002414-181002421
48	HEY1	chr1:181002182-181002604	K562	blood:	n/a	n/a
49	POLR2A	chr1:181002125-181003425	GM12878	blood:	n/a	n/a
50	MAZ	chr1:181002173-181003429	K562	blood:	n/a	chr1:181003414-181003424

No.	Distal block	Cell Line	Cell type
1	chr1:180997971..181011022-chr1:181054648..181063248,33	K562	blood:
2	chr1:180999745..181016101-chr1:181055432..181063450,33	K562	blood:
3	chr1:181001424..181004556-chr1:181055509..181058224,3	MCF-7	breast:
4	chr1:180990026..180993643-chr1:180999560..181003140,8	K562	blood:

Variant related genes	Relation type
MR1	TF binding region
ENSG00000272198	Chromatin interaction
ENSG00000135823	Chromatin interaction
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10157092	0.86[JPT][hapmap]
rs10159067	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10159443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs10218681	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12134601	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16856661	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16856663	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34260849	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3806283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3845422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3892173	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55764324	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55903939	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56030303	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56089565	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6658363	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535177	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3806284	STX6	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180992200-181003600	Weak transcription	Gastric	stomach
2	chr1:181001600-181002800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:181001600-181003000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:181001800-181002600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:181001800-181002600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:181001800-181002600	Enhancers	Brain Angular Gyrus	brain
7	chr1:181001800-181002600	Enhancers	Fetal Intestine Large	intestine
8	chr1:181001800-181002600	Enhancers	Fetal Thymus	thymus
9	chr1:181001800-181002600	Enhancers	Right Atrium	heart
10	chr1:181001800-181002600	Enhancers	HMEC	breast
11	chr1:181001800-181002600	Enhancers	NHDF-Ad	bronchial
12	chr1:181001800-181002800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:181001800-181002800	Enhancers	Fetal Intestine Small	intestine
14	chr1:181001800-181002800	Enhancers	Placenta	Placenta
15	chr1:181001800-181002800	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:181001800-181003200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:181001800-181005800	Enhancers	Spleen	Spleen
18	chr1:181002000-181002600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:181002000-181002600	Enhancers	NHLF	lung
20	chr1:181002000-181002800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr1:181002000-181002800	Flanking Active TSS	Brain Cingulate Gyrus	brain
22	chr1:181002000-181002800	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr1:181002000-181006200	Enhancers	Small Intestine	intestine
24	chr1:181002200-181002600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:181002200-181002600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:181002200-181002600	Flanking Active TSS	Liver	Liver
27	chr1:181002200-181002600	Enhancers	Fetal Muscle Trunk	muscle
28	chr1:181002200-181002600	Enhancers	Fetal Muscle Leg	muscle
29	chr1:181002200-181002600	Enhancers	Left Ventricle	heart
30	chr1:181002200-181002600	Enhancers	Psoas Muscle	Psoas
31	chr1:181002200-181002600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr1:181002200-181002600	Enhancers	Right Ventricle	heart
33	chr1:181002200-181002600	Enhancers	Thymus	Thymus
34	chr1:181002200-181002600	Flanking Active TSS	HepG2	liver
35	chr1:181002200-181002600	Enhancers	HSMM	muscle
36	chr1:181002200-181002600	Enhancers	HSMMtube	muscle
37	chr1:181002200-181002600	Enhancers	HUVEC	blood vessel
38	chr1:181002200-181002800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:181002200-181002800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr1:181002200-181002800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr1:181002200-181002800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr1:181002200-181002800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr1:181002200-181002800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:181002200-181002800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:181002200-181002800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:181002200-181002800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr1:181002200-181002800	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr1:181002200-181002800	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr1:181002200-181002800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:181002200-181002800	Enhancers	Esophagus	oesophagus

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