Variant report

Variant	rs9469039
Chromosome Location	chr6:31679242-31679243
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	GATA2	chr6:31678940-31679262	HUVEC	blood vessel:	n/a	n/a
2	SPI1	chr6:31678995-31679251	K562	blood:	n/a	chr6:31678995-31679008
3	GATA1	chr6:31678697-31679610	PBDE	blood:	n/a	n/a
4	SPI1	chr6:31678909-31679412	HL-60	blood:	n/a	chr6:31678995-31679008
5	ELF1	chr6:31678899-31679320	K562	blood:	n/a	n/a
6	MAX	chr6:31678901-31679284	K562	blood:	n/a	n/a
7	MYC	chr6:31679101-31679308	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:31679198-31679321	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31676949..31679536-chr6:31784835..31786344,2	MCF-7	breast:
2	chr6:31632238..31634263-chr6:31678523..31680253,2	MCF-7	breast:
3	chr6:31677895..31680160-chr6:31702614..31704121,2	MCF-7	breast:
4	chr6:31669599..31672574-chr6:31678491..31681695,4	MCF-7	breast:

Variant related genes	Relation type
LY6G6D	TF binding region
ENSG00000204435	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000204427	Chromatin interaction
ENSG00000204438	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10947225	1.00[AFR][1000 genomes]
rs17201459	1.00[AMR][1000 genomes]
rs28445017	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56194675	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58368425	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59402363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73728948	1.00[AMR][1000 genomes]
rs73728988	1.00[AFR][1000 genomes]
rs73728991	1.00[AFR][1000 genomes]
rs73729004	1.00[AMR][1000 genomes]
rs73729005	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9282875	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9332712	1.00[AFR][1000 genomes]
rs9461723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9461730	1.00[AFR][1000 genomes]
rs9469030	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469035	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469037	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501148	1.00[AMR][1000 genomes]
rs9501150	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501151	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501153	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601609	chr6:31280101-31799786	Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
2	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
3	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
5	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
7	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
9	nsv432868	chr6:31338844-31721033	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
10	nsv1021747	chr6:31386219-31907266	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	330 gene(s)	inside rSNPs	diseases
11	nsv884418	chr6:31525448-31741078	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
12	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
13	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
14	esv3428142	chr6:31615800-31881809	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	257 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31671600-31681600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:31671800-31695800	Weak transcription	Right Atrium	heart
3	chr6:31672000-31682800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:31672000-31685400	Weak transcription	Gastric	stomach
5	chr6:31677600-31682400	Enhancers	K562	blood
6	chr6:31677600-31683600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:31677800-31679400	Enhancers	Lung	lung
8	chr6:31677800-31680000	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:31677800-31680200	Enhancers	Spleen	Spleen
10	chr6:31677800-31680600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:31678200-31679400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:31678200-31679600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr6:31678200-31679600	Enhancers	Fetal Thymus	thymus
14	chr6:31678200-31680200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:31678200-31680200	Enhancers	Primary B cells from peripheral blood	blood
16	chr6:31678400-31679400	Enhancers	Colonic Mucosa	Colon
17	chr6:31678400-31679400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:31678400-31679600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr6:31678400-31679800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr6:31678400-31680200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:31678400-31680400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:31678400-31683200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr6:31678400-31684200	Enhancers	Fetal Brain Male	brain
24	chr6:31678600-31679400	Enhancers	Primary B cells from cord blood	blood
25	chr6:31678600-31679400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:31678600-31679400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:31678600-31679400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:31678600-31679400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr6:31678600-31679400	Flanking Active TSS	Fetal Brain Female	brain
30	chr6:31678600-31679600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:31678600-31679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr6:31678600-31679600	Enhancers	HUVEC	blood vessel
33	chr6:31678600-31679600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr6:31678600-31679800	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr6:31678600-31680200	Enhancers	Placenta	Placenta
36	chr6:31678600-31680200	Enhancers	Stomach Mucosa	stomach
37	chr6:31678800-31679400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr6:31678800-31679600	Enhancers	HMEC	breast
39	chr6:31678800-31679800	Enhancers	Primary T cells from cord blood	blood
40	chr6:31678800-31679800	Enhancers	Duodenum Mucosa	Duodenum
41	chr6:31678800-31680000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr6:31678800-31680000	Weak transcription	Pancreas	Pancrea
43	chr6:31678800-31680200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:31678800-31681200	Weak transcription	Thymus	Thymus
45	chr6:31679000-31679400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:31679000-31679600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:31679000-31679600	Flanking Active TSS	NHEK	skin
48	chr6:31679000-31680000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr6:31679000-31680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:31679000-31681200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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