Variant report

Variant	rs7226248
Chromosome Location	chr17:59939001-59939002
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	GATA3	chr17:59938482-59942100	MCF-7	breast:	n/a	chr17:59941440-59941447 chr17:59941286-59941295 chr17:59940695-59940705
2	GATA3	chr17:59938936-59941431	SK-N-SH	brain:	n/a	chr17:59941286-59941295 chr17:59940695-59940705
3	RFX5	chr17:59938285-59941998	SK-N-SH	brain:	n/a	chr17:59938788-59938796
4	E2F4	chr17:59938928-59941841	MCF10A-Er-Src	breast:	n/a	chr17:59940878-59940889 chr17:59940879-59940891 chr17:59940886-59940898 chr17:59940931-59940940
5	ZNF217	chr17:59938782-59941900	MCF-7	breast:	n/a	n/a
6	TEAD4	chr17:59939000-59941868	A549	lung:	n/a	n/a
7	POLR2A	chr17:59938795-59941376	MCF10A-Er-Src	breast:	n/a	n/a
8	SRF	chr17:59938399-59942321	MCF-7	breast:	n/a	chr17:59942006-59942021 chr17:59942008-59942019 chr17:59942009-59942018 chr17:59942007-59942018 chr17:59942005-59942019 chr17:59940890-59940900 chr17:59942009-59942020 chr17:59942005-59942023 chr17:59942007-59942020 chr17:59939748-59939766 chr17:59942005-59942022 chr17:59942008-59942025
9	GATA3	chr17:59938941-59939830	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr17:59935970-59945500	MCF-7	breast:	n/a	chr17:59941440-59941447 chr17:59941286-59941295 chr17:59940695-59940705
11	NR2F2	chr17:59938354-59942307	MCF-7	breast:	n/a	n/a
12	POLR2A	chr17:59938547-59941418	MCF10A-Er-Src	breast:	n/a	n/a
13	GATA3	chr17:59938095-59940506	MCF-7	breast:	n/a	n/a
14	NR2F2	chr17:59937915-59942311	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:59938126..59942484-chr20:52208111..52210732,4	MCF-7	breast:
2	chr17:58160448..58162938-chr17:59938931..59941632,2	MCF-7	breast:
3	chr17:59938249..59942766-chr17:60140265..60145745,10	MCF-7	breast:
4	chr1:117602136..117603845-chr17:59938886..59941004,2	MCF-7	breast:
5	chr17:59936074..59944748-chr20:55835834..55847370,36	MCF-7	breast:
6	chr17:59938658..59940749-chr7:99004886..99006495,2	MCF-7	breast:
7	chr17:59937475..59939110-chr20:55817376..55819720,2	MCF-7	breast:
8	chr17:59936983..59940866-chr17:60141087..60143647,5	MCF-7	breast:
9	chr17:59929026..59944759-chr20:55831267..55853908,71	MCF-7	breast:
10	chr11:62605730..62607893-chr17:59936927..59940452,3	MCF-7	breast:
11	chr17:59476206..59478986-chr17:59937418..59941494,6	MCF-7	breast:
12	chr1:27215485..27217208-chr17:59938995..59940925,2	MCF-7	breast:
13	chr17:59938976..59941909-chr17:60142630..60144812,2	K562	blood:
14	chr17:59486255..59492170-chr17:59932286..59941695,13	MCF-7	breast:

Variant related genes	Relation type
BRIP1	TF binding region
ENSG00000261040	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000108510	Chromatin interaction
ENSG00000142751	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000116830	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10401014	1.00[EUR][1000 genomes]
rs16945750	1.00[EUR][1000 genomes]
rs28431006	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4988342	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58025472	1.00[EUR][1000 genomes]
rs58046635	1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504075	0.84[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6504076	1.00[EUR][1000 genomes]
rs6504078	1.00[EUR][1000 genomes]
rs7211128	1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7212884	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7213026	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7221827	1.00[EUR][1000 genomes]
rs7222876	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7224112	1.00[EUR][1000 genomes]
rs73991952	1.00[EUR][1000 genomes]
rs8065060	1.00[EUR][1000 genomes]
rs8068267	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069386	0.92[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	1.00[EUR][1000 genomes]
rs9783841	1.00[EUR][1000 genomes]
rs9892063	0.86[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9892123	1.00[EUR][1000 genomes]
rs9894718	1.00[EUR][1000 genomes]
rs9896768	1.00[EUR][1000 genomes]
rs9899042	1.00[EUR][1000 genomes]
rs9899780	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9902699	1.00[EUR][1000 genomes]
rs9903562	1.00[EUR][1000 genomes]
rs9905888	1.00[EUR][1000 genomes]
rs9909145	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9909882	0.86[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9910067	1.00[EUR][1000 genomes]
rs9910252	1.00[EUR][1000 genomes]
rs9910902	1.00[EUR][1000 genomes]
rs9913351	1.00[TSI][hapmap]
rs9914007	1.00[EUR][1000 genomes]
rs9914605	1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9916070	1.00[TSI][hapmap]
rs9944467	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59898800-59939600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr17:59898800-59939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:59906200-59940200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:59912200-59939200	Weak transcription	HSMM	muscle
5	chr17:59912200-59939800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:59912400-59939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:59912400-59940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:59912400-59940400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr17:59917800-59939200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr17:59920400-59940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:59921200-59939800	Weak transcription	Thymus	Thymus
12	chr17:59921600-59940000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:59923200-59939800	Weak transcription	Fetal Muscle Leg	muscle
14	chr17:59923600-59940200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr17:59924800-59939200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr17:59926200-59940200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr17:59926400-59939200	Weak transcription	Fetal Brain Female	brain
18	chr17:59927400-59939200	Weak transcription	Fetal Kidney	kidney
19	chr17:59931600-59939800	Weak transcription	Primary B cells from cord blood	blood
20	chr17:59932200-59940200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:59933400-59940400	Weak transcription	Pancreas	Pancrea
22	chr17:59933800-59939400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr17:59934000-59939200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr17:59935000-59940200	Weak transcription	Ovary	ovary
25	chr17:59936800-59939400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:59937000-59939600	Weak transcription	Fetal Intestine Small	intestine
27	chr17:59937000-59939800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr17:59937200-59940200	Weak transcription	Small Intestine	intestine
29	chr17:59937600-59940200	Weak transcription	Esophagus	oesophagus
30	chr17:59937800-59939200	Weak transcription	Fetal Thymus	thymus
31	chr17:59938000-59939200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:59938400-59939800	Flanking Active TSS	NHLF	lung
33	chr17:59938400-59941400	Active TSS	GM12878-XiMat	blood
34	chr17:59938600-59939200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr17:59938600-59939400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
36	chr17:59938600-59939600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:59938600-59939800	Enhancers	Fetal Lung	lung
38	chr17:59938600-59940400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr17:59938600-59941400	Active TSS	Brain Germinal Matrix	brain
40	chr17:59938800-59939200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr17:59938800-59939200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:59938800-59939200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr17:59938800-59939200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr17:59938800-59939200	Enhancers	Fetal Stomach	stomach
45	chr17:59938800-59939400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr17:59938800-59939400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr17:59938800-59939400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr17:59938800-59939400	Enhancers	Fetal Heart	heart
49	chr17:59938800-59939600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:59938800-59939800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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