Variant report

Variant	rs28498495
Chromosome Location	chr8:95540983-95540984
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	SIN3AK20	chr8:95540607-95541708	MCF-7	breast:	n/a	n/a
2	EP300	chr8:95540767-95541480	MCF-7	breast:	n/a	chr8:95541107-95541117 chr8:95541121-95541135
3	TCF7L2	chr8:95540869-95541300	MCF-7	breast:	n/a	n/a
4	EP300	chr8:95540923-95541346	K562	blood:	n/a	chr8:95541107-95541117 chr8:95541121-95541135
5	JUND	chr8:95540965-95541269	K562	blood:	n/a	chr8:95541045-95541057
6	EP300	chr8:95540895-95541335	T-47D	breast:	n/a	chr8:95541107-95541117 chr8:95541121-95541135
7	EP300	chr8:95540776-95541400	T-47D	breast:	n/a	chr8:95541107-95541117 chr8:95541121-95541135
8	ZNF217	chr8:95540892-95541399	MCF-7	breast:	n/a	n/a
9	HDAC2	chr8:95540851-95541562	MCF-7	breast:	n/a	chr8:95541108-95541117
10	RAD21	chr8:95540835-95541341	MCF-7	breast:	n/a	n/a
11	TAL1	chr8:95540982-95541182	K562	blood:	n/a	n/a
12	TEAD4	chr8:95540757-95541399	MCF-7	breast:	n/a	n/a
13	ESR1	chr8:95540868-95541322	T-47D	breast:	n/a	n/a
14	GATA3	chr8:95540884-95541465	MCF-7	breast:	n/a	n/a
15	GATA3	chr8:95540669-95541609	MCF-7	breast:	n/a	n/a
16	JUND	chr8:95540721-95541481	T-47D	breast:	n/a	chr8:95541045-95541057
17	GATA3	chr8:95540788-95541476	T-47D	breast:	n/a	n/a
18	GATA3	chr8:95540834-95541400	T-47D	breast:	n/a	n/a
19	TEAD4	chr8:95540805-95541402	MCF-7	breast:	n/a	n/a
20	NR2F2	chr8:95540738-95541471	MCF-7	breast:	n/a	n/a
21	GATA3	chr8:95540528-95541676	MCF-7	breast:	n/a	n/a
22	JUND	chr8:95540794-95541460	T-47D	breast:	n/a	chr8:95541045-95541057
23	SIN3AK20	chr8:95540606-95541632	MCF-7	breast:	n/a	n/a
24	FOXA1	chr8:95540852-95541332	T-47D	breast:	n/a	chr8:95541112-95541124 chr8:95541108-95541120
25	FOXA1	chr8:95540843-95541386	T-47D	breast:	n/a	chr8:95541112-95541124 chr8:95541108-95541120
26	GATA3	chr8:95540886-95541634	MCF-7	breast:	n/a	n/a
27	HDAC2	chr8:95540809-95541497	MCF-7	breast:	n/a	chr8:95541108-95541117
28	RCOR1	chr8:95540911-95541441	K562	blood:	n/a	n/a
29	POLR2A	chr8:95540704-95541104	K562	blood:	n/a	n/a
30	NR2F2	chr8:95540742-95541548	MCF-7	breast:	n/a	n/a
31	ESR1	chr8:95540892-95541327	T-47D	breast:	n/a	n/a
32	GATA2	chr8:95540914-95541223	K562	blood:	n/a	n/a
33	FOXM1	chr8:95540853-95541540	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:95536103..95541001-chr8:95541149..95546680,4	MCF-7	breast:
2	chr8:95539636..95541198-chr8:95564562..95567296,2	MCF-7	breast:
3	chr8:95540816..95542532-chr8:95731372..95733184,2	MCF-7	breast:
4	chr8:95539618..95543703-chr8:95563899..95568056,6	MCF-7	breast:
5	chr8:95533781..95536601-chr8:95538847..95541074,2	K562	blood:
6	chr8:95539392..95541672-chr8:95550945..95553259,2	MCF-7	breast:
7	chr8:95539818..95541551-chr8:95651175..95653324,2	MCF-7	breast:

Variant related genes	Relation type
KIAA1429	TF binding region
ENSG00000254315	TF binding region
ENSG00000253704	Chromatin interaction
ENSG00000104413	Chromatin interaction
ENSG00000261437	Chromatin interaction
ENSG00000156162	Chromatin interaction
ENSG00000254315	Chromatin interaction
ENSG00000164944	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10086307	0.96[EUR][1000 genomes]
rs10086311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10087221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10089982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10090029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10090628	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10093542	0.96[EUR][1000 genomes]
rs10094155	1.00[EUR][1000 genomes]
rs10094298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10094477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10095474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10095883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10097107	0.96[EUR][1000 genomes]
rs10098298	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10098682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10102139	0.96[EUR][1000 genomes]
rs10103436	0.96[EUR][1000 genomes]
rs10104301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10104797	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10105476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10106455	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10110389	0.96[EUR][1000 genomes]
rs10111251	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10111789	0.91[AMR][1000 genomes]
rs10217108	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10441536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10441537	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1055798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12334369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12334578	0.96[EUR][1000 genomes]
rs12334783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12334844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12334990	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12335104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13438933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13438940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13439154	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13439558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13439676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2119461	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2381883	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28386976	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28397924	0.96[EUR][1000 genomes]
rs28406352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28409018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28420254	0.96[EUR][1000 genomes]
rs28436849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28449797	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28475734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28480604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28481457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28502182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28524089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28526027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28539788	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28542193	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28563951	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28572173	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28608052	0.96[EUR][1000 genomes]
rs28634264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28666401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28681034	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28775004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28791815	0.83[AMR][1000 genomes]
rs28805925	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28848914	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs28897138	0.91[AMR][1000 genomes]
rs3136421	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4567002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56859277	0.96[EUR][1000 genomes]
rs57897120	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6992902	0.96[EUR][1000 genomes]
rs6998829	0.96[EUR][1000 genomes]
rs73695616	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73695617	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73695619	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73695620	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73695622	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73695624	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73698013	0.96[EUR][1000 genomes]
rs7835534	1.00[AFR][1000 genomes]
rs8117	1.00[EUR][1000 genomes]
rs9297938	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95493000-95549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:95495600-95541000	Weak transcription	Esophagus	oesophagus
3	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr8:95498400-95554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:95499400-95552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:95501200-95541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:95516800-95554600	Strong transcription	Fetal Thymus	thymus
8	chr8:95520400-95555200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr8:95520600-95552400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:95527600-95548600	Strong transcription	Fetal Muscle Leg	muscle
11	chr8:95528000-95542400	Weak transcription	Pancreas	Pancrea
12	chr8:95528400-95541200	Weak transcription	Right Ventricle	heart
13	chr8:95528400-95542400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:95532800-95558800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr8:95534000-95543600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr8:95534200-95545000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr8:95535400-95556000	Weak transcription	Fetal Heart	heart
18	chr8:95535800-95549800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr8:95535800-95555600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr8:95536000-95555600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr8:95536200-95541000	Weak transcription	Stomach Mucosa	stomach
22	chr8:95536200-95549200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr8:95536400-95552200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr8:95536600-95541400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr8:95536600-95542400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr8:95536600-95557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr8:95536800-95543200	Strong transcription	Rectal Smooth Muscle	rectum
28	chr8:95536800-95543400	Strong transcription	Brain Germinal Matrix	brain
29	chr8:95536800-95546600	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr8:95536800-95549800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr8:95536800-95550600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr8:95536800-95551400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr8:95536800-95552400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr8:95536800-95556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr8:95537000-95541600	Strong transcription	Fetal Kidney	kidney
36	chr8:95537000-95541800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:95537000-95541800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr8:95537000-95543400	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr8:95537000-95543600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr8:95537000-95543600	Strong transcription	A549	lung
41	chr8:95537000-95544400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr8:95537000-95545200	Strong transcription	Fetal Brain Female	brain
43	chr8:95537000-95545200	Strong transcription	HepG2	liver
44	chr8:95537000-95547000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr8:95537000-95547800	Strong transcription	Brain Anterior Caudate	brain
46	chr8:95537000-95548000	Strong transcription	Thymus	Thymus
47	chr8:95537000-95548400	Strong transcription	Brain Hippocampus Middle	brain
48	chr8:95537000-95548400	Strong transcription	Hela-S3	cervix
49	chr8:95537000-95549000	Strong transcription	GM12878-XiMat	blood
50	chr8:95537000-95549400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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