Variant report

Variant	rs2668769
Chromosome Location	chr18:44780454-44780455
allele	C/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	REST	chr18:44780418-44781625	H1-hESC	embryonic stem cell:	n/a	chr18:44781123-44781141 chr18:44780958-44780971 chr18:44781122-44781142 chr18:44781128-44781142 chr18:44781130-44781140 chr18:44781127-44781136 chr18:44781122-44781142 chr18:44781122-44781142 chr18:44781122-44781131
2	REST	chr18:44780352-44782710	HL-60	blood:	n/a	chr18:44781123-44781141 chr18:44780958-44780971 chr18:44781122-44781142 chr18:44781128-44781142 chr18:44781130-44781140 chr18:44781127-44781136 chr18:44781122-44781142 chr18:44781122-44781142 chr18:44781122-44781131
3	REST	chr18:44780372-44780658	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:44778191..44780835-chr18:44785176..44787814,2	K562	blood:
2	chr18:44778191..44780835-chr18:44785049..44787814,3	K562	blood:
3	chr18:44779645..44782742-chr18:44785627..44788634,4	MCF-7	breast:

Variant related genes	Relation type
SKOR2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12326579	0.81[ASN][1000 genomes]
rs16950348	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16950349	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668765	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668766	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668773	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668774	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668775	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2684815	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2684816	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2684827	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684828	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684829	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684844	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2684848	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2684849	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2684850	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2684854	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684855	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684856	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56313614	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv828226	chr18:44762014-44801196	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv1794744	chr18:44774077-44788908	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1797427	chr18:44774077-44788908	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1835264	chr18:44774077-44788908	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1839014	chr18:44774077-44788908	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1819372	chr18:44774673-44799515	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2668769	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44778400-44780600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
2	chr18:44778400-44780800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
3	chr18:44778400-44781000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
4	chr18:44778400-44781400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr18:44779400-44781000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
6	chr18:44779600-44782800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr18:44779800-44780800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr18:44780200-44781400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:44780400-44780600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:44780400-44780600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr18:44780400-44781000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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