Variant report

Variant	rs11582552
Chromosome Location	chr1:169865009-169865010
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	chr1:169864848-169865187	GM12878	blood:	n/a	n/a
2	JUN	chr1:169861838-169865596	K562	blood:	n/a	chr1:169863455-169863464 chr1:169863451-169863464 chr1:169863477-169863486
3	BATF	chr1:169864809-169865538	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169863583..169866323-chr1:169872602..169875354,3	MCF-7	breast:
2	chr1:169862596..169865250-chr1:170499667..170504019,5	K562	blood:
3	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
4	chr1:169863487..169865405-chr1:169882715..169884373,2	K562	blood:
5	chr1:169763994..169765974-chr1:169862962..169865288,2	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000231407	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000120370	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10489175	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10800488	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11577641	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11578817	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11579102	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11579709	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11581959	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11585093	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11589659	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11589671	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590604	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1572551	0.98[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16828209	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16862683	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16862705	0.86[EUR][1000 genomes]
rs2420510	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2420511	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34657513	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35196850	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753312	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3766138	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766139	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766145	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766146	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766150	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3817859	0.86[EUR][1000 genomes]
rs4656201	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4656720	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656722	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656723	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4656726	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4656727	0.88[EUR][1000 genomes]
rs55806711	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57805301	0.86[EUR][1000 genomes]
rs58111285	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60191157	0.86[EUR][1000 genomes]
rs60315765	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61806076	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61807812	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61807813	0.85[EUR][1000 genomes]
rs61807814	0.82[EUR][1000 genomes]
rs61807817	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61807818	0.86[EUR][1000 genomes]
rs61807835	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61807840	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685211	0.86[EUR][1000 genomes]
rs73026253	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription 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	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169863400-169865400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:169863800-169868400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:169864000-169865400	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:169864000-169865400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:169864000-169865400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:169864000-169865600	Enhancers	GM12878-XiMat	blood
7	chr1:169864000-169868800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169864000-169869000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:169864000-169869000	Weak transcription	HMEC	breast
10	chr1:169864200-169865400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:169864200-169866400	Enhancers	K562	blood
12	chr1:169864200-169867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:169864200-169868400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:169864200-169869000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:169864400-169868200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:169864600-169865600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr1:169864800-169865400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr1:169865000-169866400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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