Variant report

Variant	rs4712880
Chromosome Location	chr6:25028066-25028067
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	PML	chr6:25027265-25028091	GM12878	blood:	n/a	chr6:25027910-25027919
2	RUNX3	chr6:25027281-25028203	GM12878	blood:	n/a	n/a
3	EBF1	chr6:25027066-25028137	GM12878	blood:	n/a	chr6:25028076-25028085
4	ELF1	chr6:25027427-25028085	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:25027968-25028132	MCF-7	breast:	n/a	n/a
6	NRF1	chr6:25027946-25028130	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25027553..25029661-chr6:25041949..25043586,2	MCF-7	breast:

Variant related genes	Relation type
ASS1P1	TF binding region
ENSG00000111913	Chromatin interaction
ENSG00000272053	Chromatin interaction
ENSG00000229313	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10806997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946741	0.82[EUR][1000 genomes]
rs10946742	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394360	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712879	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6918101	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	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
4	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
5	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
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
2	chr6:25024800-25028200	Enhancers	NHEK	skin
3	chr6:25024800-25028400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:25025000-25028600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:25025200-25028600	Enhancers	Fetal Thymus	thymus
6	chr6:25025400-25028400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:25026000-25028200	Enhancers	Fetal Lung	lung
8	chr6:25026400-25033600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:25026800-25028200	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:25027000-25028200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:25027000-25028200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr6:25027000-25028200	Flanking Active TSS	Dnd41	blood
13	chr6:25027000-25028400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
14	chr6:25027000-25028600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:25027000-25028600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:25027200-25028200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr6:25027400-25028200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:25027400-25028200	Flanking Active TSS	Primary B cells from peripheral blood	blood
19	chr6:25027400-25028200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr6:25027400-25028400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr6:25027400-25028400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:25027400-25028400	Enhancers	Lung	lung
23	chr6:25027600-25028200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr6:25027600-25028200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:25027600-25028200	Enhancers	Placenta	Placenta
26	chr6:25027600-25028400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:25027800-25028200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:25027800-25028200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:25027800-25028200	Enhancers	Thymus	Thymus
30	chr6:25027800-25028800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:25027800-25029200	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:25028000-25028200	Enhancers	Primary B cells from cord blood	blood
33	chr6:25028000-25028200	Enhancers	Primary T cells from cord blood	blood
34	chr6:25028000-25028200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:25028000-25028200	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr6:25028000-25028200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:25028000-25028400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:25028000-25028400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr6:25028000-25028600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:25028000-25028600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:25028000-25030600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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