Variant report

Variant	rs17558727
Chromosome Location	chr6:106530848-106530849
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	BCL3	chr6:106530571-106530990	GM12878	blood:	n/a	n/a
2	E2F4	chr6:106530502-106530930	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr6:106530562-106531000	MCF10A-Er-Src	breast:	n/a	chr6:106530854-106530868
4	FOS	chr6:106530554-106530965	MCF10A-Er-Src	breast:	n/a	chr6:106530854-106530868
5	CEBPB	chr6:106530615-106530975	IMR90	lung:	n/a	n/a
6	FOS	chr6:106530617-106530947	MCF10A-Er-Src	breast:	n/a	chr6:106530854-106530868
7	FOSL2	chr6:106530473-106531073	SK-N-SH	brain:	n/a	chr6:106530854-106530868
8	STAT3	chr6:106530667-106530891	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr6:106530774-106530974	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr6:106530639-106530863	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr6:106530668-106530933	MCF10A-Er-Src	breast:	n/a	n/a
12	MEF2A	chr6:106530429-106531063	SK-N-SH	brain:	n/a	chr6:106530716-106530731 chr6:106530717-106530728 chr6:106530715-106530731 chr6:106530445-106530461 chr6:106530716-106530730 chr6:106530719-106530728 chr6:106530714-106530735 chr6:106530714-106530735 chr6:106530718-106530729 chr6:106530478-106530495
13	TCF12	chr6:106530422-106531106	SK-N-SH	brain:	n/a	n/a
14	MYC	chr6:106530618-106530913	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr6:106530555-106530955	MCF10A-Er-Src	breast:	n/a	chr6:106530854-106530868
16	PBX3	chr6:106530661-106530863	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:106530816-106530922	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:106525524..106527475-chr6:106529699..106532511,2	K562	blood:
2	chr6:106453872..106456221-chr6:106529003..106530917,2	K562	blood:
3	chr6:106524677..106527761-chr6:106528087..106531603,5	K562	blood:

Variant related genes	Relation type
PRDM1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12663005	1.00[AMR][1000 genomes]
rs17558797	1.00[AMR][1000 genomes]
rs3804332	1.00[ASW][hapmap]
rs3890556	1.00[AMR][1000 genomes]
rs4336479	0.92[ASN][1000 genomes]
rs4443535	0.92[ASN][1000 genomes]
rs6913893	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9320148	1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[ASN][1000 genomes]
rs9373830	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9384600	1.00[AMR][1000 genomes]
rs9386511	1.00[AMR][1000 genomes]
rs9398059	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9398063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9398065	1.00[AMR][1000 genomes]
rs9398066	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1025231	chr6:106451012-106634389	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription 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 target site	9 gene(s)	inside rSNPs	diseases
3	nsv830755	chr6:106461705-106624202	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1025900	chr6:106529777-106898421	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106528200-106532200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:106528600-106532600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr6:106528800-106532200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:106528800-106533600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:106529000-106532200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:106529000-106532400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:106529200-106532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:106529200-106532400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:106529600-106531200	Enhancers	Dnd41	blood
10	chr6:106529600-106532400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:106529800-106532000	Enhancers	NHDF-Ad	bronchial
12	chr6:106529800-106532200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:106529800-106533000	Enhancers	NHLF	lung
14	chr6:106529800-106534000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:106530000-106532200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:106530000-106533200	Enhancers	NHEK	skin
17	chr6:106530200-106533800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:106530400-106531200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:106530400-106531400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:106530400-106533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:106530400-106533200	Enhancers	HMEC	breast
22	chr6:106530400-106533200	Enhancers	NH-A	brain
23	chr6:106530400-106533200	Enhancers	Osteobl	bone
24	chr6:106530400-106533400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:106530400-106533800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr6:106530600-106531000	Bivalent Enhancer	Fetal Lung	lung
27	chr6:106530600-106531000	Enhancers	Ovary	ovary
28	chr6:106530600-106531000	Enhancers	HSMMtube	muscle
29	chr6:106530600-106532400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:106530600-106533200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:106530600-106533200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:106530600-106533400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:106530600-106533400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:106530600-106533400	Enhancers	HSMM	muscle
35	chr6:106530600-106533600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr6:106530600-106533800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr6:106530600-106533800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:106530600-106533800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr6:106530600-106533800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:106530800-106531000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr6:106530800-106531000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:106530800-106531000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:106530800-106531000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:106530800-106531000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:106530800-106531000	Enhancers	Psoas Muscle	Psoas
46	chr6:106530800-106531000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:106530800-106531000	Enhancers	Small Intestine	intestine
48	chr6:106530800-106531200	Enhancers	Primary T cells from cord blood	blood
49	chr6:106530800-106531600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:106530800-106532200	Genic enhancers	Fetal Intestine Large	intestine

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