Variant report

Variant	rs1570413
Chromosome Location	chr1:197410295-197410296
allele	G/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	chr1:197409678-197410311	SK-N-SH	brain:	n/a	n/a
2	EP300	chr1:197409811-197410370	Hela-S3	cervix:	n/a	n/a
3	RFX5	chr1:197409813-197410315	Hela-S3	cervix:	n/a	n/a
4	GATA1	chr1:197409844-197411704	K562	blood:	n/a	n/a
5	MAFK	chr1:197409634-197410333	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr1:197409814-197410308	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr1:197409737-197410470	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
CRB1	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1022908	1.00[AMR][1000 genomes]
rs1033826	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494753	0.87[AMR][1000 genomes]
rs10754226	1.00[MEX][hapmap];0.83[MKK][hapmap]
rs10801606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10922235	1.00[AMR][1000 genomes]
rs12089070	0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs1362940	1.00[MEX][hapmap]
rs1421390	1.00[AMR][1000 genomes]
rs1421391	1.00[AMR][1000 genomes]
rs1421394	1.00[AMR][1000 genomes]
rs1570412	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1592707	1.00[AMR][1000 genomes]
rs1592708	1.00[AMR][1000 genomes]
rs1862011	0.83[MKK][hapmap]
rs1923758	0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1923760	1.00[YRI][hapmap]
rs1923761	0.96[AFR][1000 genomes]
rs1923763	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs1951697	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1998433	1.00[AMR][1000 genomes]
rs2146484	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2146485	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160967	1.00[AMR][1000 genomes]
rs2181373	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256222	0.92[YRI][hapmap]
rs2359119	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2476016	0.92[AFR][1000 genomes]
rs2476017	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2476018	0.92[YRI][hapmap]
rs2476022	0.96[AFR][1000 genomes]
rs2476024	0.85[AFR][1000 genomes]
rs2494272	0.96[AFR][1000 genomes]
rs2759660	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2821099	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2821100	0.96[AFR][1000 genomes]
rs2821105	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs2821124	1.00[MEX][hapmap]
rs3888104	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3902057	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244150	0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4335404	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4428919	0.87[AMR][1000 genomes]
rs4989560	1.00[AMR][1000 genomes]
rs516640	1.00[MEX][hapmap]
rs6428401	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6428402	1.00[AMR][1000 genomes]
rs6428403	0.87[AMR][1000 genomes]
rs6428405	1.00[AMR][1000 genomes]
rs6428406	1.00[AMR][1000 genomes]
rs6656674	1.00[AMR][1000 genomes]
rs6664766	1.00[AMR][1000 genomes]
rs6670147	1.00[AMR][1000 genomes]
rs6678776	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6684593	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6686241	1.00[AMR][1000 genomes]
rs6689739	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690015	0.87[AMR][1000 genomes]
rs6691940	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6694254	1.00[AMR][1000 genomes]
rs7514167	0.92[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7515749	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7525737	0.87[AMR][1000 genomes]
rs7530158	1.00[AMR][1000 genomes]
rs927511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs942050	0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9427667	0.89[AFR][1000 genomes]
rs980370	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs980371	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197403800-197413000	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:197404200-197412600	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:197404600-197411200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:197406000-197412200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:197406800-197411200	Enhancers	Hela-S3	cervix
6	chr1:197407200-197411200	Weak transcription	Aorta	Aorta
7	chr1:197407200-197411800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:197407600-197411200	Weak transcription	Brain Germinal Matrix	brain
9	chr1:197407600-197414200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:197407800-197411000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:197407800-197411200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:197407800-197413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:197408400-197411000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:197408400-197411000	Weak transcription	Fetal Heart	heart
15	chr1:197408400-197411200	Weak transcription	Fetal Lung	lung
16	chr1:197408400-197412200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:197409200-197410800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:197409200-197411000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:197409400-197411200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:197409400-197412400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:197409600-197411400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:197409600-197412200	Enhancers	H9 Cell Line	embryonic stem cell
23	chr1:197409800-197411000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:197409800-197414000	Weak transcription	Brain Anterior Caudate	brain
25	chr1:197410000-197410800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:197410000-197410800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:197410000-197411800	Enhancers	NH-A	brain
28	chr1:197410200-197410600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:197410200-197410600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:197410200-197411000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:197410200-197414000	Weak transcription	Ovary	ovary
32	chr1:197410200-197417000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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