Variant report

Variant	rs6559178
Chromosome Location	chr8:6593019-6593020
allele	A/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	POLR2A	chr8:6592084-6593334	GM12878	blood:	n/a	n/a
2	ZNF143	chr8:6592863-6593032	GM12878	blood:	n/a	n/a
3	JUN	chr8:6592935-6593025	K562	blood:	n/a	n/a
4	POLR2A	chr8:6591864-6593025	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:6590798..6593095-chr8:6599894..6603696,3	K562	blood:
2	chr8:6585868..6588138-chr8:6590976..6594012,3	K562	blood:
3	chr8:6591889..6594476-chr8:6597879..6600037,2	K562	blood:
4	chr8:6592860..6594827-chr8:6613486..6615924,2	K562	blood:

Variant related genes	Relation type
AGPAT5	TF binding region
ENSG00000266038	Chromatin interaction
ENSG00000155189	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10096753	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10110103	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1365042	0.85[CEU][hapmap]
rs1559744	0.83[CEU][hapmap]
rs1559748	0.85[CEU][hapmap]
rs1961768	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1971312	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2408444	0.87[CEU][hapmap]
rs2911970	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2911971	0.93[CHB][hapmap]
rs2911975	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2911976	0.86[CEU][hapmap]
rs2911977	0.86[CEU][hapmap]
rs2911978	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2911979	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2911980	0.82[CEU][hapmap]
rs2912054	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2928576	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2928579	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2928623	0.86[CEU][hapmap]
rs2928625	0.82[CEU][hapmap]
rs2928626	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2928629	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2928630	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2928631	0.93[ASN][1000 genomes]
rs2936502	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2936505	0.80[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2936506	0.81[ASN][1000 genomes]
rs2936507	1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2936512	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936520	0.82[CEU][hapmap]
rs2980658	0.84[ASN][1000 genomes]
rs2980679	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2980680	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2980683	0.86[CEU][hapmap]
rs2980684	0.86[CEU][hapmap]
rs2980688	0.92[CHB][hapmap];0.82[JPT][hapmap]
rs2980689	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs2980690	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3780087	0.86[CEU][hapmap]
rs6559177	0.84[EUR][1000 genomes]
rs7015837	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv1025976	chr8:6472948-6686972	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription 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	15 gene(s)	inside rSNPs	diseases
10	nsv933768	chr8:6482944-6618221	Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	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
12	nsv1030637	chr8:6545498-6669949	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
13	nsv1034115	chr8:6546984-6665832	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	13 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv1031063	chr8:6570354-6622685	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
17	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
18	nsv1024685	chr8:6575334-6622685	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6568000-6603400	Weak transcription	Fetal Brain Male	brain
2	chr8:6582600-6594600	Strong transcription	Hela-S3	cervix
3	chr8:6585800-6615800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:6587200-6604600	Weak transcription	NHEK	skin
5	chr8:6587200-6617000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr8:6587600-6599400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr8:6587600-6608000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr8:6587800-6596200	Strong transcription	Dnd41	blood
9	chr8:6587800-6605200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr8:6587800-6607400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr8:6587800-6612000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr8:6587800-6617000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr8:6588000-6596200	Strong transcription	Fetal Thymus	thymus
14	chr8:6588200-6596000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:6588400-6597400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr8:6588600-6607400	Weak transcription	Spleen	Spleen
17	chr8:6589000-6598200	Weak transcription	Liver	Liver
18	chr8:6589400-6594000	Genic enhancers	K562	blood
19	chr8:6589800-6596200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr8:6590200-6593200	Strong transcription	Primary T cells from cord blood	blood
21	chr8:6590200-6596000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr8:6590400-6604800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr8:6590600-6593200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr8:6590800-6593200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr8:6590800-6593200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr8:6591000-6593600	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr8:6591000-6594200	Weak transcription	Right Atrium	heart
28	chr8:6591000-6594400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr8:6591000-6602000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr8:6591000-6602000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr8:6591000-6604600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:6591000-6605200	Weak transcription	Fetal Brain Female	brain
33	chr8:6591000-6614200	Weak transcription	Left Ventricle	heart
34	chr8:6591000-6617400	Weak transcription	Psoas Muscle	Psoas
35	chr8:6591200-6594000	Weak transcription	Fetal Heart	heart
36	chr8:6591200-6594000	Weak transcription	Right Ventricle	heart
37	chr8:6591200-6594400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr8:6591200-6594800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr8:6591200-6599000	Weak transcription	HMEC	breast
40	chr8:6591200-6601800	Weak transcription	Brain Hippocampus Middle	brain
41	chr8:6591200-6602000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr8:6591200-6602000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr8:6591200-6602000	Weak transcription	Colon Smooth Muscle	Colon
44	chr8:6591200-6602000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr8:6591200-6602800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr8:6591200-6603600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr8:6591200-6607200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr8:6591200-6607200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr8:6591200-6614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr8:6591200-6625400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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