Variant report

Variant	rs8077724
Chromosome Location	chr17:38678106-38678107
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	TCF12	chr17:38677562-38678362	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr17:38677668-38678280	Hela-S3	cervix:	n/a	n/a
3	FOS	chr17:38677622-38678292	MCF10A-Er-Src	breast:	n/a	chr17:38678116-38678126 chr17:38678117-38678125 chr17:38678116-38678127 chr17:38678116-38678126
4	RFX5	chr17:38677886-38678207	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr17:38677446-38678241	U87	brain:	n/a	n/a
6	ESR1	chr17:38677730-38678260	ECC-1	luminal epithelium:	n/a	chr17:38678001-38678016
7	FOXA2	chr17:38677582-38678316	A549	lung:	n/a	n/a
8	SIN3AK20	chr17:38677626-38678399	A549	lung:	n/a	n/a
9	POLR2A	chr17:38677697-38678193	Hela-S3	cervix:	n/a	n/a
10	GABPA	chr17:38677263-38678188	SK-N-SH	brain:	n/a	n/a
11	MYC	chr17:38677672-38678271	MCF10A-Er-Src	breast:	n/a	n/a
12	EP300	chr17:38677436-38678470	ECC-1	luminal epithelium:	n/a	chr17:38677984-38677997
13	GABPA	chr17:38677426-38678119	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr17:38677679-38678235	HCT-116	colon:	n/a	n/a
15	POLR2A	chr17:38677617-38678352	Hela-S3	cervix:	n/a	n/a
16	SIX5	chr17:38677524-38678162	A549	lung:	n/a	n/a
17	STAT3	chr17:38677781-38678162	MCF10A-Er-Src	breast:	n/a	chr17:38677792-38677804
18	PRDM1	chr17:38677996-38678258	Hela-S3	cervix:	n/a	n/a
19	TCF7L2	chr17:38677735-38678286	Hela-S3	cervix:	n/a	chr17:38678117-38678126
20	FOSL2	chr17:38677597-38678303	A549	lung:	n/a	chr17:38678116-38678126 chr17:38678117-38678125 chr17:38678116-38678127 chr17:38678116-38678126
21	TEAD4	chr17:38677682-38678195	ECC-1	luminal epithelium:	n/a	n/a
22	ZBTB33	chr17:38677531-38678282	A549	lung:	n/a	n/a
23	POLR2A	chr17:38677614-38679548	MCF10A-Er-Src	breast:	n/a	n/a
24	ELK1	chr17:38677596-38678248	Hela-S3	cervix:	n/a	n/a
25	EP300	chr17:38677793-38678297	Hela-S3	cervix:	n/a	chr17:38677984-38677997
26	SMC3	chr17:38677687-38678219	Hela-S3	cervix:	n/a	n/a
27	MAZ	chr17:38676785-38679269	IMR90	lung:	n/a	chr17:38676819-38676828 chr17:38676817-38676825 chr17:38676821-38676828 chr17:38677127-38677137
28	STAT3	chr17:38677657-38678313	MCF10A-Er-Src	breast:	n/a	chr17:38677792-38677804
29	CREB1	chr17:38677532-38678210	A549	lung:	n/a	n/a
30	ELF1	chr17:38677503-38678170	A549	lung:	n/a	chr17:38677748-38677761
31	SMARCC1	chr17:38676841-38678463	Hela-S3	cervix:	n/a	chr17:38678117-38678126
32	MAFK	chr17:38677825-38678147	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr17:38677411-38678274	IMR90	lung:	n/a	n/a
34	ZKSCAN1	chr17:38677599-38678333	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr17:38677596-38678320	IMR90	lung:	n/a	n/a
36	ELF1	chr17:38677519-38678305	A549	lung:	n/a	chr17:38677748-38677761
37	FOS	chr17:38677668-38678297	MCF10A-Er-Src	breast:	n/a	chr17:38678116-38678126 chr17:38678117-38678125 chr17:38678116-38678127 chr17:38678116-38678126
38	RAD21	chr17:38677679-38678251	A549	lung:	n/a	n/a
39	NR3C1	chr17:38677628-38678187	A549	lung:	n/a	chr17:38678117-38678126
40	POLR2A	chr17:38677498-38678226	HCT-116	colon:	n/a	n/a
41	USF1	chr17:38677505-38678295	A549	lung:	n/a	n/a
42	NFIC	chr17:38677620-38678352	ECC-1	luminal epithelium:	n/a	n/a
43	BCL3	chr17:38677511-38678395	A549	lung:	n/a	n/a
44	GATA3	chr17:38677036-38678353	A549	lung:	n/a	n/a
45	REST	chr17:38677751-38678193	SK-N-SH	brain:	n/a	chr17:38677903-38677921
46	TEAD4	chr17:38677660-38678356	ECC-1	luminal epithelium:	n/a	n/a
47	ESR1	chr17:38677735-38678229	ECC-1	luminal epithelium:	n/a	chr17:38678001-38678016
48	ETS1	chr17:38677674-38678313	A549	lung:	n/a	n/a
49	SIX5	chr17:38677243-38678765	A549	lung:	n/a	n/a
50	FOSL2	chr17:38677483-38678363	SK-N-SH	brain:	n/a	chr17:38678116-38678126 chr17:38678117-38678125 chr17:38678116-38678127 chr17:38678116-38678126

No.	Distal block	Cell Line	Cell type
1	chr17:38676796..38678412-chr17:38763235..38765302,2	MCF-7	breast:
2	chr17:38678096..38679987-chr17:38715270..38716866,2	MCF-7	breast:
3	chr17:38654640..38659414-chr17:38673768..38679140,6	MCF-7	breast:
4	chr17:38647398..38649761-chr17:38676727..38678938,2	K562	blood:
5	chr17:38639539..38641673-chr17:38677366..38679503,2	K562	blood:
6	chr17:38600130..38602545-chr17:38675909..38679796,4	MCF-7	breast:
7	chr17:38676325..38680650-chr17:38704875..38709448,7	MCF-7	breast:
8	chr17:38676381..38678576-chr17:38679743..38681770,2	K562	blood:
9	chr17:38677625..38680142-chr17:38696757..38698899,2	MCF-7	breast:
10	chr17:38569801..38571878-chr17:38675987..38678508,2	K562	blood:
11	chr17:38571667..38573665-chr17:38677679..38680655,2	K562	blood:
12	chr17:38629814..38633387-chr17:38676751..38679736,4	MCF-7	breast:
13	chr17:38675352..38677497-chr17:38677864..38681564,3	MCF-7	breast:
14	chr17:38671928..38674313-chr17:38677766..38679421,2	MCF-7	breast:
15	chr17:38677974..38679924-chr17:38691519..38693332,2	MCF-7	breast:
16	chr17:38673127..38676333-chr17:38678075..38682047,4	K562	blood:

Variant related genes	Relation type
ENSG00000266088	TF binding region
ENSG00000266088	Chromatin interaction
ENSG00000131746	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1072070	1.00[ASN][1000 genomes]
rs11871009	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16965880	1.00[YRI][hapmap]
rs28493507	1.00[EUR][1000 genomes]
rs4092050	1.00[MEX][hapmap]
rs4890086	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs4890088	0.83[ASN][1000 genomes]
rs499490	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs594783	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60411936	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503543	1.00[MEX][hapmap]
rs7208120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7208316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7212543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7219622	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7221799	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs73310952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73983076	0.83[ASN][1000 genomes]
rs73983078	1.00[ASN][1000 genomes]
rs8064741	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8066508	1.00[CEU][hapmap]
rs8069091	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs896136	1.00[MEX][hapmap]
rs9675320	1.00[CHB][hapmap]

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	nsv1058185	chr17:38629339-38689908	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv3369555	chr17:38677926-38681324	Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38668400-38680600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:38671400-38679800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38671600-38679400	Enhancers	Placenta	Placenta
4	chr17:38672200-38679200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr17:38672600-38680800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr17:38672800-38679200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:38673600-38678200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:38673800-38678200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:38674000-38679200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:38674200-38681200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr17:38675000-38679400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr17:38675400-38679200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr17:38675400-38680800	Enhancers	HMEC	breast
14	chr17:38675600-38686600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:38675800-38679200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:38676800-38678200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr17:38677000-38678200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr17:38677000-38678400	Enhancers	NHLF	lung
19	chr17:38677000-38679000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:38677000-38679200	Enhancers	HSMMtube	muscle
21	chr17:38677000-38679600	Enhancers	Dnd41	blood
22	chr17:38677000-38680800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:38677200-38678400	Flanking Active TSS	Hela-S3	cervix
24	chr17:38677200-38678400	Enhancers	NHDF-Ad	bronchial
25	chr17:38677200-38678600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:38677200-38678600	Enhancers	NH-A	brain
27	chr17:38677200-38678800	Enhancers	Osteobl	bone
28	chr17:38677200-38679800	Enhancers	Esophagus	oesophagus
29	chr17:38677400-38678200	Enhancers	Fetal Thymus	thymus
30	chr17:38677400-38678400	Flanking Active TSS	A549	lung
31	chr17:38677400-38678600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr17:38677400-38678600	Enhancers	K562	blood
33	chr17:38677400-38679200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:38677400-38679200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:38677400-38679800	Weak transcription	Primary B cells from cord blood	blood
36	chr17:38677600-38678200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:38677600-38678400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr17:38677600-38678800	Flanking Active TSS	NHEK	skin
39	chr17:38677600-38682200	Weak transcription	Spleen	Spleen
40	chr17:38677600-38687800	Weak transcription	Right Ventricle	heart
41	chr17:38677800-38678200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr17:38677800-38678200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:38677800-38678200	Enhancers	Lung	lung
44	chr17:38677800-38678200	Bivalent Enhancer	HepG2	liver
45	chr17:38677800-38680600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:38678000-38678200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr17:38678000-38678200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:38678000-38678200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr17:38678000-38678200	Enhancers	Thymus	Thymus
50	chr17:38678000-38678400	Flanking Active TSS	HSMM	muscle

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