Variant report

Variant	rs628794
Chromosome Location	chr6:24945077-24945078
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	SETDB1	chr6:24944940-24945879	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000217083	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12202529	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12216261	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626145	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16889835	0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs1753511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1813711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs216256	0.88[ASN][1000 genomes]
rs216257	0.90[ASN][1000 genomes]
rs216258	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs216260	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs216261	0.83[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs216262	0.86[ASN][1000 genomes]
rs370748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413203	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs413610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415025	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419288	0.91[ASN][1000 genomes]
rs421817	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431796	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs441957	0.84[CEU][hapmap]
rs495157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs614837	0.84[YRI][hapmap]
rs614900	0.85[YRI][hapmap]
rs640380	0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs640845	0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs644722	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644748	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685008	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7738180	0.85[YRI][hapmap]
rs7742242	0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7775482	0.85[YRI][hapmap]
rs9356949	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379698	0.95[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	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking 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	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs628794	GPLD1	cis	cerebellum	SCAN
rs628794	HIST1H2BE	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24941400-24946200	Weak transcription	Fetal Thymus	thymus
2	chr6:24942400-24948000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:24942600-24945800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:24943200-24945800	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
5	chr6:24943800-24945200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr6:24943800-24945200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
7	chr6:24943800-24945800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr6:24943800-24945800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr6:24943800-24945800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
10	chr6:24943800-24946000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
11	chr6:24943800-24946000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr6:24943800-24948000	ZNF genes & repeats	Dnd41	blood
13	chr6:24944000-24945600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
14	chr6:24944000-24946000	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:24944000-24946000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:24944200-24945800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:24944600-24945200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:24944800-24949200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:24945000-24946800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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