Variant report

Variant	rs562425
Chromosome Location	chr6:150359199-150359200
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	SUZ12	chr6:150358565-150359685	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PHBP1	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10155731	0.85[ASN][1000 genomes]
rs11155696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11155697	0.94[ASN][1000 genomes]
rs11752529	0.94[ASN][1000 genomes]
rs11752629	0.90[ASN][1000 genomes]
rs11754987	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11757186	0.92[ASN][1000 genomes]
rs1194970	0.81[AFR][1000 genomes]
rs12204988	0.81[ASN][1000 genomes]
rs13198863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13209192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1543547	0.92[ASN][1000 genomes]
rs1853664	0.92[ASN][1000 genomes]
rs34006533	0.94[ASN][1000 genomes]
rs3860823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4086064	0.94[ASN][1000 genomes]
rs5006620	0.93[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs563278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs61730071	0.81[ASN][1000 genomes]
rs72561813	0.83[ASN][1000 genomes]
rs763574	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9478362	0.85[ASN][1000 genomes]
rs9478380	0.94[ASN][1000 genomes]
rs9479403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9479404	0.85[ASN][1000 genomes]
rs9479405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9479429	0.91[ASN][1000 genomes]
rs9479478	0.93[ASN][1000 genomes]
rs9479481	0.94[ASN][1000 genomes]
rs9479482	0.94[ASN][1000 genomes]
rs9479513	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv7375	chr6:150324114-150388625	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3344440	chr6:150324131-150388650	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3323918	chr6:150327978-150392099	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv886766	chr6:150335407-150364009	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv886767	chr6:150335407-150400488	Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv5535	chr6:150339697-150361659	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv886768	chr6:150340035-150366143	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv886769	chr6:150346037-150364009	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150358200-150359200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
2	chr6:150358200-150359400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
3	chr6:150358200-150359800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:150358200-150359800	Bivalent Enhancer	Fetal Brain Male	brain
5	chr6:150358400-150359200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr6:150358400-150359400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
7	chr6:150358400-150359600	Bivalent Enhancer	Fetal Heart	heart
8	chr6:150358400-150359600	Bivalent Enhancer	Fetal Muscle Leg	muscle
9	chr6:150358400-150359800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:150358400-150359800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
11	chr6:150358400-150360200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:150358600-150359200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
17	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
18	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
20	chr6:150358600-150359200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
21	chr6:150358600-150359200	Bivalent/Poised TSS	HSMM	muscle
22	chr6:150358600-150359400	Bivalent Enhancer	Colonic Mucosa	Colon
23	chr6:150358600-150359400	Flanking Active TSS	Ovary	ovary
24	chr6:150358600-150359400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
25	chr6:150358600-150359400	Bivalent Enhancer	Spleen	Spleen
26	chr6:150358600-150359400	Bivalent Enhancer	HUVEC	blood vessel
27	chr6:150358600-150359600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:150358600-150359600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr6:150358600-150359600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
30	chr6:150358600-150359600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:150358600-150359600	Bivalent Enhancer	Fetal Stomach	stomach
32	chr6:150358600-150359600	Enhancers	Gastric	stomach
33	chr6:150358600-150359600	Flanking Active TSS	Right Ventricle	heart
34	chr6:150358600-150359600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
35	chr6:150358600-150359600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
36	chr6:150358600-150359800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:150358600-150359800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr6:150358600-150359800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
39	chr6:150358600-150359800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
40	chr6:150358600-150359800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:150358600-150359800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
42	chr6:150358600-150359800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:150358600-150359800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr6:150358600-150359800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:150358600-150359800	Bivalent Enhancer	Liver	Liver
46	chr6:150358600-150359800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr6:150358600-150359800	Active TSS	Right Atrium	heart
48	chr6:150358600-150359800	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr6:150358600-150360000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr6:150358600-150360000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links