Variant report

Variant	rs17412982
Chromosome Location	chr4:96007796-96007797
allele	G/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	FOS	chr4:96007714-96008025	MCF10A-Er-Src	breast:	n/a	n/a
2	FOXA1	chr4:96007694-96008043	T-47D	breast:	n/a	chr4:96007938-96007950
3	NR2F2	chr4:96007620-96008243	MCF-7	breast:	n/a	n/a
4	STAT3	chr4:96007778-96008029	MCF10A-Er-Src	breast:	n/a	n/a
5	SP1	chr4:96007627-96008157	A549	lung:	n/a	n/a
6	FOS	chr4:96007688-96008071	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr4:96007643-96008219	MCF-7	breast:	n/a	n/a
8	GATA3	chr4:96007729-96007988	MCF-7	breast:	n/a	n/a
9	FOS	chr4:96007762-96008025	MCF10A-Er-Src	breast:	n/a	n/a
10	TCF12	chr4:96007557-96008241	A549	lung:	n/a	chr4:96007925-96007933
11	FOXM1	chr4:96007619-96008311	MCF-7	breast:	n/a	n/a
12	GATA3	chr4:96007631-96008122	T-47D	breast:	n/a	n/a
13	FOXM1	chr4:96007689-96008206	MCF-7	breast:	n/a	n/a
14	EP300	chr4:96007632-96008196	MCF-7	breast:	n/a	n/a
15	GATA3	chr4:96007733-96008007	MCF-7	breast:	n/a	n/a
16	JUND	chr4:96007604-96008241	MCF-7	breast:	n/a	n/a
17	GABPA	chr4:96007693-96008125	MCF-7	breast:	n/a	n/a
18	TEAD4	chr4:96007723-96008205	MCF-7	breast:	n/a	n/a
19	TCF12	chr4:96007403-96008334	MCF-7	breast:	n/a	chr4:96007925-96007933
20	TCF12	chr4:96007613-96008283	MCF-7	breast:	n/a	chr4:96007925-96007933
21	CEBPB	chr4:96007692-96008147	MCF-7	breast:	n/a	n/a
22	GATA3	chr4:96007570-96008137	A549	lung:	n/a	n/a
23	JUND	chr4:96007601-96008174	T-47D	breast:	n/a	n/a
24	ESR1	chr4:96007715-96008158	T-47D	breast:	n/a	n/a
25	ZNF217	chr4:96007692-96008090	MCF-7	breast:	n/a	n/a
26	GATA3	chr4:96007582-96008254	MCF-7	breast:	n/a	n/a
27	POLR2A	chr4:96007776-96007982	MCF10A-Er-Src	breast:	n/a	n/a
28	TCF7L2	chr4:96007661-96008115	MCF-7	breast:	n/a	chr4:96007789-96007805 chr4:96007793-96007800 chr4:96007789-96007805
29	EP300	chr4:96007667-96008258	T-47D	breast:	n/a	n/a
30	GATA3	chr4:96007557-96008132	T-47D	breast:	n/a	n/a
31	NR2F2	chr4:96007619-96008157	MCF-7	breast:	n/a	n/a
32	SIN3AK20	chr4:96007439-96008313	MCF-7	breast:	n/a	n/a
33	FOXA1	chr4:96007656-96008201	T-47D	breast:	n/a	chr4:96007938-96007950
34	MAX	chr4:96007681-96008036	MCF-7	breast:	n/a	n/a
35	FOS	chr4:96007703-96008103	MCF10A-Er-Src	breast:	n/a	n/a
36	HDAC2	chr4:96007787-96008026	MCF-7	breast:	n/a	chr4:96007941-96007950
37	STAT3	chr4:96007689-96008029	MCF10A-Er-Src	breast:	n/a	n/a
38	FOSL2	chr4:96007630-96008113	MCF-7	breast:	n/a	n/a
39	MYC	chr4:96007739-96008060	MCF10A-Er-Src	breast:	n/a	n/a
40	EP300	chr4:96007514-96008251	A549	lung:	n/a	n/a
41	TEAD4	chr4:96007724-96008120	MCF-7	breast:	n/a	n/a
42	EP300	chr4:96007697-96008077	A549	lung:	n/a	n/a
43	FOSL2	chr4:96007738-96008167	MCF-7	breast:	n/a	n/a
44	SIN3AK20	chr4:96007576-96008260	MCF-7	breast:	n/a	n/a
45	ESR1	chr4:96007694-96008138	T-47D	breast:	n/a	n/a
46	CEBPB	chr4:96007741-96008042	MCF-7	breast:	n/a	n/a
47	HDAC2	chr4:96007630-96008172	MCF-7	breast:	n/a	chr4:96007941-96007950
48	GATA3	chr4:96007217-96008444	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:95970827..95973009-chr4:96005064..96008963,3	MCF-7	breast:
2	chr4:96004208..96009283-chr4:96010834..96014104,5	MCF-7	breast:
3	chr4:95912061..95914592-chr4:96007501..96009488,2	MCF-7	breast:

Variant related genes	Relation type
BMPR1B	TF binding region
ENSG00000138696	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1073308	0.91[ASN][1000 genomes]
rs11934798	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11937369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500473	0.87[LWK][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs12645001	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13434647	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1434549	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17022918	0.86[CHD][hapmap]
rs17023017	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17344835	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[YRI][hapmap];0.89[EUR][1000 genomes]
rs17412559	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863652	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1961224	0.92[CEU][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3796432	0.88[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs3796434	0.86[JPT][hapmap]
rs6815044	1.00[YRI][hapmap]
rs6831697	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs6832300	0.94[YRI][hapmap]
rs72672718	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7664797	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.90[EUR][1000 genomes]
rs7679627	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7680852	0.96[CEU][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs9997720	0.83[EUR][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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv492312	chr4:95823124-96128327	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer 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 target site	2 gene(s)	inside rSNPs	diseases
5	nsv830011	chr4:95947560-96103934	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv594907	chr4:95975470-96170439	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96003800-96011600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:96004800-96009200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:96005600-96008400	Enhancers	HMEC	breast
4	chr4:96005600-96008800	Flanking Active TSS	Dnd41	blood
5	chr4:96005600-96009000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:96005600-96009600	Enhancers	NHEK	skin
7	chr4:96006600-96007800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:96006600-96009200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:96006800-96008000	Enhancers	Primary T cells from cord blood	blood
10	chr4:96006800-96008400	Weak transcription	Stomach Mucosa	stomach
11	chr4:96006800-96009200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:96006800-96015400	Weak transcription	HUVEC	blood vessel
13	chr4:96007000-96007800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:96007000-96008200	Active TSS	Fetal Thymus	thymus
15	chr4:96007000-96008200	Flanking Active TSS	A549	lung
16	chr4:96007000-96009400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:96007000-96014000	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:96007200-96009200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:96007200-96009600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:96007400-96008000	Flanking Active TSS	Thymus	Thymus
21	chr4:96007400-96009800	Enhancers	Hela-S3	cervix
22	chr4:96007600-96008000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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