Variant report

Variant	rs2146485
Chromosome Location	chr1:197407439-197407440
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	GATA3	chr1:197407069-197407861	SH-SY5Y	brain:	n/a	chr1:197407425-197407432 chr1:197407425-197407432 chr1:197407425-197407432 chr1:197407418-197407439
2	POLR2A	chr1:197407225-197407684	SK-N-MC	brain:	n/a	n/a
3	GATA3	chr1:197407213-197407587	T-47D	breast:	n/a	chr1:197407425-197407432 chr1:197407425-197407432 chr1:197407425-197407432 chr1:197407418-197407439
4	EP300	chr1:197406856-197408130	SK-N-SH	brain:	n/a	n/a
5	GATA2	chr1:197407067-197407938	SH-SY5Y	brain:	n/a	chr1:197407425-197407432 chr1:197407425-197407432 chr1:197407425-197407432 chr1:197407418-197407439
6	EP300	chr1:197407059-197407843	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr1:197406992-197407900	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197401163..197403684-chr1:197406748..197408451,2	K562	blood:
2	chr1:197406975..197410030-chr1:197411436..197415376,3	K562	blood:

Variant related genes	Relation type
CRB1	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1022908	1.00[AMR][1000 genomes]
rs1033826	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494753	0.87[AMR][1000 genomes]
rs10801606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10922235	1.00[AMR][1000 genomes]
rs12089070	0.87[AMR][1000 genomes]
rs1421390	1.00[AMR][1000 genomes]
rs1421391	1.00[AMR][1000 genomes]
rs1421394	1.00[AMR][1000 genomes]
rs1570412	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1570413	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]
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	0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2160967	1.00[AMR][1000 genomes]
rs2181373	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256222	0.93[YRI][hapmap]
rs2359119	0.89[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	0.93[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	0.92[YRI][hapmap]
rs3888104	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3902057	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4244150	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	0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs4989560	1.00[AMR][1000 genomes]
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[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	0.96[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	0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs7530158	1.00[AMR][1000 genomes]
rs927511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs942050	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[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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197402600-197409200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:197403400-197410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:197403800-197413000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:197404000-197407800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:197404200-197412600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:197404600-197409000	Weak transcription	Brain Anterior Caudate	brain
7	chr1:197404600-197409800	Weak transcription	Ovary	ovary
8	chr1:197404600-197411200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:197405800-197407600	Enhancers	Brain Germinal Matrix	brain
10	chr1:197405800-197409000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:197406000-197408600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr1:197406000-197412200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:197406200-197407800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:197406200-197408400	Enhancers	Fetal Lung	lung
15	chr1:197406200-197410200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:197406400-197408000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:197406400-197408600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:197406600-197407600	Enhancers	Fetal Brain Female	brain
19	chr1:197406600-197408200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:197406800-197411200	Enhancers	Hela-S3	cervix
21	chr1:197407200-197407600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:197407200-197408400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:197407200-197409000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:197407200-197411200	Weak transcription	Aorta	Aorta
25	chr1:197407200-197411800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:197407400-197407600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:197407400-197408400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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