Variant report

Variant	rs579438
Chromosome Location	chr1:170116042-170116043
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	KAP1	chr1:170114760-170116217	HEK293	kidney:	n/a	chr1:170115175-170115183
2	POLR2A	chr1:170116014-170116299	H1-neurons	neurons:	n/a	n/a
3	RUNX3	chr1:170116041-170116385	GM12878	blood:	n/a	n/a
4	TCF7L2	chr1:170114729-170116321	HEK293	kidney:	n/a	chr1:170116141-170116157

Variant related genes	Relation type
MIR3119-1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10800501	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1411464	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2786921	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656205	0.90[ASN][1000 genomes]
rs471155	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs471569	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471781	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs482571	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs493966	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs495125	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs495524	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs504942	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs514257	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs522361	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs523222	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524309	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs525285	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs532141	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs533387	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548356	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548582	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs550297	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551042	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs556764	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs563559	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs572480	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575119	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs576152	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704499	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9427182	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv999310	chr1:170065943-170223350	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170114200-170116200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:170114200-170116800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:170114200-170117000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:170114600-170116800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:170114600-170117000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:170114800-170116200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:170114800-170116200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:170114800-170116400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:170114800-170116400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:170114800-170116800	Enhancers	Primary T cells from cord blood	blood
11	chr1:170115000-170116200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:170115000-170116400	Active TSS	Right Atrium	heart
13	chr1:170115000-170116600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:170115000-170116600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
15	chr1:170115000-170116800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:170115000-170116800	Flanking Active TSS	Dnd41	blood
17	chr1:170115200-170116200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:170115200-170116200	Enhancers	NH-A	brain
19	chr1:170115400-170119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:170115600-170116200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:170115600-170116200	Active TSS	Brain Germinal Matrix	brain
22	chr1:170115600-170117800	Weak transcription	Osteobl	bone
23	chr1:170115800-170116200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:170115800-170116200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
25	chr1:170115800-170116200	Flanking Active TSS	Fetal Heart	heart
26	chr1:170115800-170116800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:170116000-170116600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
28	chr1:170116000-170116600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell

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