Variant report

Variant	rs552778
Chromosome Location	chr1:155687277-155687278
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	GATA3	chr1:155687094-155687283	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
DAP3	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10908468	0.84[EUR][1000 genomes]
rs1094462	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11803678	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13374129	0.95[EUR][1000 genomes]
rs1624846	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16837037	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16837063	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs171167	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17370773	1.00[CEU][hapmap]
rs17377506	0.85[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1749415	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1749417	0.82[AMR][1000 genomes]
rs1749421	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1765284	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1962247	1.00[EUR][1000 genomes]
rs2477541	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2686255	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28574887	0.95[EUR][1000 genomes]
rs2985708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs348206	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35044707	0.95[EUR][1000 genomes]
rs41264969	1.00[EUR][1000 genomes]
rs4253908	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4612618	0.95[EUR][1000 genomes]
rs4933	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4971065	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4971086	0.87[EUR][1000 genomes]
rs4971087	0.87[EUR][1000 genomes]
rs4971106	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs543854	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs548809	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56758819	0.95[EUR][1000 genomes]
rs59706606	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59791187	0.95[EUR][1000 genomes]
rs598176	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs61258690	0.90[EUR][1000 genomes]
rs621181	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs682020	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs708612	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73001021	0.95[EUR][1000 genomes]
rs7525057	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7535158	0.95[EUR][1000 genomes]
rs822016	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs822018	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs822019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs822020	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs822022	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs822026	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs822477	0.96[YRI][hapmap]
rs822495	1.00[CEU][hapmap]
rs822497	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs822516	1.00[GIH][hapmap]
rs822523	0.96[AMR][1000 genomes]
rs9426929	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9427223	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv547965	chr1:155563152-155688600	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv3381327	chr1:155582853-155718436	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv3436971	chr1:155618172-155733386	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	esv3338099	chr1:155618190-155733359	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
9	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv3065	chr1:155682768-155727524	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155660200-155698800	Weak transcription	NHLF	lung
2	chr1:155660400-155688800	Weak transcription	Lung	lung
3	chr1:155660400-155706200	Weak transcription	Colonic Mucosa	Colon
4	chr1:155661600-155688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:155661600-155707800	Weak transcription	HUVEC	blood vessel
6	chr1:155663200-155701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:155665200-155708000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:155665400-155695000	Weak transcription	Pancreas	Pancrea
9	chr1:155665400-155699000	Weak transcription	Right Ventricle	heart
10	chr1:155665600-155707200	Weak transcription	Psoas Muscle	Psoas
11	chr1:155665800-155707000	Weak transcription	Small Intestine	intestine
12	chr1:155667600-155689600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:155669200-155702200	Weak transcription	Gastric	stomach
14	chr1:155672800-155698800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:155673200-155695000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:155673800-155707800	Weak transcription	Aorta	Aorta
17	chr1:155676000-155695000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:155676400-155689400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:155676400-155691800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:155676400-155695400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:155676400-155698600	Weak transcription	Stomach Mucosa	stomach
22	chr1:155676400-155706200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:155677200-155691400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:155677400-155705200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:155678800-155689000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr1:155679200-155687400	Strong transcription	Hela-S3	cervix
27	chr1:155679200-155688600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:155679200-155688800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:155679200-155689600	Weak transcription	Thymus	Thymus
30	chr1:155679200-155691800	Weak transcription	Ovary	ovary
31	chr1:155679400-155688000	Weak transcription	Brain Anterior Caudate	brain
32	chr1:155679400-155710400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:155679800-155688600	Weak transcription	Fetal Lung	lung
34	chr1:155679800-155695200	Weak transcription	Fetal Brain Female	brain
35	chr1:155679800-155704200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:155681400-155688000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:155681400-155688000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:155681400-155688400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:155681600-155696800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:155681600-155707800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:155681800-155687600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:155681800-155687600	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:155681800-155688800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:155681800-155689800	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:155681800-155690200	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:155681800-155693600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:155682000-155690200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:155682200-155692000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:155682400-155690600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:155682600-155687600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links