Variant report

Variant	rs9469989
Chromosome Location	chr6:35280785-35280786
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	SPI1	chr6:35280646-35281069	HL-60	blood:	n/a	chr6:35280801-35280808 chr6:35280903-35280916
2	MAFK	chr6:35280639-35280834	HepG2	liver:	n/a	chr6:35280725-35280736 chr6:35280724-35280735 chr6:35280720-35280736 chr6:35280723-35280737
3	POLR2A	chr6:35280486-35280932	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:35271752..35272749-chr6:35280146..35281158,10	MCF-7	breast:
2	chr6:35279156..35280875-chr6:35287560..35289237,2	MCF-7	breast:
3	chr6:35271891..35272664-chr6:35280221..35281099,4	MCF-7	breast:
4	chr6:35278958..35282229-chr6:35283892..35290479,5	K562	blood:

Variant related genes	Relation type
DEF6	TF binding region
ENSG00000023892	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11571503	1.00[EUR][1000 genomes]
rs16868699	0.84[AMR][1000 genomes]
rs2284197	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs45482297	0.84[AMR][1000 genomes]
rs61415782	1.00[EUR][1000 genomes]
rs73409758	0.84[AMR][1000 genomes]
rs73745161	1.00[EUR][1000 genomes]
rs73748060	1.00[EUR][1000 genomes]
rs7746988	1.00[CEU][hapmap]
rs9658062	1.00[EUR][1000 genomes]
rs9658107	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9658114	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9658115	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9658128	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9658133	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9658143	1.00[EUR][1000 genomes]
rs9658147	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9658176	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 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	chr6:35265200-35285600	Weak transcription	Brain Substantia Nigra	brain
2	chr6:35271400-35285000	Weak transcription	HepG2	liver
3	chr6:35271600-35285200	Weak transcription	Fetal Intestine Large	intestine
4	chr6:35271600-35285600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:35272400-35284600	Weak transcription	HMEC	breast
6	chr6:35272400-35285400	Weak transcription	Gastric	stomach
7	chr6:35276000-35293800	Weak transcription	K562	blood
8	chr6:35276800-35281000	Strong transcription	NHEK	skin
9	chr6:35277000-35281600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:35277000-35285400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:35278000-35281000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:35278200-35285600	Weak transcription	Colonic Mucosa	Colon
13	chr6:35278600-35285400	Weak transcription	Pancreas	Pancrea
14	chr6:35279000-35285400	Weak transcription	Esophagus	oesophagus
15	chr6:35279000-35285600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:35279200-35280800	Enhancers	Adipose Nuclei	Adipose
17	chr6:35279200-35282600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:35279400-35285400	Weak transcription	Right Atrium	heart
19	chr6:35279600-35282000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:35279800-35280800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr6:35279800-35281000	Strong transcription	Dnd41	blood
22	chr6:35279800-35281600	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr6:35279800-35282000	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:35279800-35282000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:35280000-35280800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr6:35280000-35280800	Genic enhancers	Fetal Thymus	thymus
27	chr6:35280000-35281000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
28	chr6:35280000-35281000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:35280000-35281800	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:35280000-35285200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:35280000-35285400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:35280200-35280800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr6:35280200-35280800	Strong transcription	GM12878-XiMat	blood
34	chr6:35280200-35281000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:35280200-35282000	Genic enhancers	Monocytes-CD14+_RO01746	blood
36	chr6:35280200-35283000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:35280200-35285200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:35280200-35285400	Weak transcription	Left Ventricle	heart
39	chr6:35280200-35285600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:35280200-35285600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:35280400-35280800	Enhancers	Duodenum Mucosa	Duodenum
42	chr6:35280400-35280800	Strong transcription	Thymus	Thymus
43	chr6:35280400-35281600	Genic enhancers	Primary B cells from cord blood	blood
44	chr6:35280400-35282000	Genic enhancers	Primary T cells fromperipheralblood	blood
45	chr6:35280400-35282000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:35280400-35283200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr6:35280400-35285000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr6:35280400-35285400	Weak transcription	Fetal Stomach	stomach
49	chr6:35280600-35280800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr6:35280600-35281200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links