Variant report

Variant	rs1188474
Chromosome Location	chr1:228613052-228613053
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	NFYB	chr1:228612986-228613192	Hela-S3	cervix:	n/a	chr1:228613105-228613120 chr1:228613106-228613116 chr1:228613103-228613118 chr1:228613144-228613159 chr1:228613104-228613118 chr1:228613103-228613118 chr1:228613146-228613161 chr1:228613145-228613159 chr1:228613144-228613159
2	TBP	chr1:228613040-228613291	H1-hESC	embryonic stem cell:	n/a	n/a
3	NFYB	chr1:228612920-228613303	K562	blood:	n/a	chr1:228613105-228613120 chr1:228613106-228613116 chr1:228613103-228613118 chr1:228613144-228613159 chr1:228613104-228613118 chr1:228613103-228613118 chr1:228613146-228613161 chr1:228613145-228613159 chr1:228613144-228613159
4	POLR2A	chr1:228612463-228613126	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:228612558-228613086	GM12892	blood:	n/a	n/a
6	NFYB	chr1:228613000-228613284	GM12878	blood:	n/a	chr1:228613105-228613120 chr1:228613106-228613116 chr1:228613103-228613118 chr1:228613144-228613159 chr1:228613104-228613118 chr1:228613103-228613118 chr1:228613146-228613161 chr1:228613145-228613159 chr1:228613144-228613159

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228353096..228354983-chr1:228611648..228613946,2	MCF-7	breast:

Variant related genes	Relation type
HIST3H3	TF binding region
ENSG00000203684	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10157289	0.83[EUR][1000 genomes]
rs10158354	0.83[EUR][1000 genomes]
rs10158680	0.83[EUR][1000 genomes]
rs10916313	0.95[ASN][1000 genomes]
rs1150917	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1150918	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11555960	0.81[EUR][1000 genomes]
rs11581974	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11587839	0.95[ASN][1000 genomes]
rs1188473	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188475	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1188482	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1188483	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188485	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188487	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188488	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1188489	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12031395	0.83[EUR][1000 genomes]
rs12061490	0.83[EUR][1000 genomes]
rs12061642	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12065660	0.83[EUR][1000 genomes]
rs12065815	0.83[EUR][1000 genomes]
rs12082349	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12085738	0.85[EUR][1000 genomes]
rs12089997	0.83[EUR][1000 genomes]
rs12093491	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12094956	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12691493	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12725863	0.95[ASN][1000 genomes]
rs12735877	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12760907	0.88[EUR][1000 genomes]
rs13373984	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2230656	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105114	0.85[EUR][1000 genomes]
rs34090141	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34673199	0.83[EUR][1000 genomes]
rs35155240	0.83[EUR][1000 genomes]
rs35711644	0.84[EUR][1000 genomes]
rs3738687	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3795814	0.83[EUR][1000 genomes]
rs4065231	0.81[EUR][1000 genomes]
rs4581279	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653551	0.94[ASN][1000 genomes]
rs4653552	0.94[ASN][1000 genomes]
rs4653960	0.88[ASN][1000 genomes]
rs474600	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493954	0.81[EUR][1000 genomes]
rs494154	0.81[EUR][1000 genomes]
rs503203	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs503391	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505129	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs513467	0.81[EUR][1000 genomes]
rs532465	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs538851	0.84[ASN][1000 genomes]
rs541959	0.83[EUR][1000 genomes]
rs56174824	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs564309	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs572442	0.84[EUR][1000 genomes]
rs573128	0.84[EUR][1000 genomes]
rs58462432	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61825312	0.83[EUR][1000 genomes]
rs61825336	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61825338	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6426501	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659690	0.95[ASN][1000 genomes]
rs6666241	0.95[ASN][1000 genomes]
rs7513530	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7524236	0.95[ASN][1000 genomes]
rs7555386	0.95[ASN][1000 genomes]
rs9787095	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv508697	chr1:228540037-228622614	Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228596400-228615400	Weak transcription	A549	lung
2	chr1:228606000-228614000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:228606000-228615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228610600-228620400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:228612200-228613400	Enhancers	Placenta	Placenta
6	chr1:228612200-228614200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:228612400-228615600	Weak transcription	HepG2	liver
8	chr1:228612600-228613200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:228612600-228613200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:228612600-228614000	Weak transcription	K562	blood
11	chr1:228612800-228616600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:228613000-228613200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:228613000-228621000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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