Variant report

Variant	rs2978894
Chromosome Location	chr8:6693629-6693630
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	POLR2A	chr8:6691757-6693654	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr8:6691293-6694197	NB4	blood:	n/a	n/a
3	MAX	chr8:6691800-6693679	NB4	blood:	n/a	chr8:6692465-6692475
4	MXI1	chr8:6691249-6694001	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AGPAT5-1	chr8:6693488-6693743	ENSG00000245857
2	lnc-AGPAT5-1	chr8:6693488-6693743	NONHSAT124793
3	lnc-AGPAT5-1	chr8:6693488-6693743	NR_045217

Variant related genes	Relation type
XKR5	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2702846	0.82[EUR][1000 genomes]
rs2741098	0.82[EUR][1000 genomes]
rs28668629	0.80[EUR][1000 genomes]
rs2951833	0.89[EUR][1000 genomes]
rs2951851	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2977798	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2977799	0.90[EUR][1000 genomes]
rs2977802	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2977803	0.95[EUR][1000 genomes]
rs2977804	0.95[EUR][1000 genomes]
rs2977806	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2978889	0.82[EUR][1000 genomes]
rs2978890	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2978892	0.90[EUR][1000 genomes]
rs2978893	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2978895	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2978898	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2978902	0.83[EUR][1000 genomes]
rs2980954	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2980955	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3863728	0.91[EUR][1000 genomes]
rs4840638	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4840639	0.84[EUR][1000 genomes]
rs9314614	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9772604	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv933075	chr8:6456475-7366650	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
9	nsv831220	chr8:6527845-6728491	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
10	nsv465436	chr8:6568201-6921404	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv610006	chr8:6568201-6921404	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv1027883	chr8:6570354-7250368	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv1034812	chr8:6578390-6920312	Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv949532	chr8:6579563-6999220	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv482865	chr8:6585920-6765111	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
16	nsv1015563	chr8:6596171-6730826	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
17	nsv539432	chr8:6596171-6730826	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv1015244	chr8:6638899-6988914	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
19	esv2752262	chr8:6638899-7011075	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
20	nsv1025587	chr8:6651912-7171085	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
21	nsv465437	chr8:6655391-6829085	Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv610007	chr8:6655391-6829085	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1031296	chr8:6673296-6920312	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	nsv890060	chr8:6690276-6717107	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6691400-6693800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr8:6691400-6694000	Active TSS	Fetal Kidney	kidney
3	chr8:6691400-6694400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:6691800-6693800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr8:6691800-6693800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr8:6693000-6698000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr8:6693200-6693800	Flanking Active TSS	Fetal Thymus	thymus
8	chr8:6693200-6694400	Flanking Active TSS	Dnd41	blood
9	chr8:6693200-6698000	Weak transcription	Brain Substantia Nigra	brain
10	chr8:6693400-6693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:6693400-6694000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:6693400-6694400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr8:6693400-6698000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr8:6693400-6698000	Weak transcription	Pancreas	Pancrea
15	chr8:6693400-6698000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr8:6693400-6698200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:6693400-6698600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr8:6693400-6698600	Weak transcription	GM12878-XiMat	blood
19	chr8:6693400-6699200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr8:6693600-6693800	Enhancers	Primary T cells from cord blood	blood
21	chr8:6693600-6693800	Enhancers	Primary hematopoietic stem cells	blood
22	chr8:6693600-6693800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr8:6693600-6693800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr8:6693600-6694000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr8:6693600-6694000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr8:6693600-6694000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr8:6693600-6694000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr8:6693600-6694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr8:6693600-6694000	Enhancers	Brain Germinal Matrix	brain
30	chr8:6693600-6694000	Enhancers	Fetal Intestine Small	intestine
31	chr8:6693600-6694000	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr8:6693600-6694000	Flanking Active TSS	Fetal Stomach	stomach
33	chr8:6693600-6694000	Enhancers	Thymus	Thymus
34	chr8:6693600-6694200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr8:6693600-6694200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr8:6693600-6694200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr8:6693600-6694200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
38	chr8:6693600-6698000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr8:6693600-6698000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr8:6693600-6698000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr8:6693600-6698000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:6693600-6698000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr8:6693600-6698000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:6693600-6698000	Weak transcription	Fetal Brain Female	brain
45	chr8:6693600-6698000	Weak transcription	Fetal Heart	heart
46	chr8:6693600-6698000	Weak transcription	Fetal Lung	lung
47	chr8:6693600-6698000	Weak transcription	Spleen	Spleen
48	chr8:6693600-6698000	Weak transcription	NH-A	brain
49	chr8:6693600-6698000	Weak transcription	Osteobl	bone

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