Variant report

Variant	rs9842960
Chromosome Location	chr3:52438268-52438269
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	POLR2A	chr3:52437938-52438424	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52438120-52438531	Hela-S3	cervix:	n/a	n/a
3	SPI1	chr3:52437870-52438296	HL-60	blood:	n/a	chr3:52438109-52438116 chr3:52438106-52438119 chr3:52438107-52438120
4	POLR2A	chr3:52437925-52438713	HL-60	blood:	n/a	n/a
5	POLR2A	chr3:52438033-52438308	K562	blood:	n/a	n/a
6	POLR2A	chr3:52438082-52438319	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52435154..52438907-chr3:52439834..52442973,4	MCF-7	breast:

Variant related genes	Relation type
BAP1	TF binding region
ENSG00000163930	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10212560	1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10440116	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10510759	1.00[MEX][hapmap]
rs10865972	1.00[YRI][hapmap]
rs1541495	1.00[YRI][hapmap]
rs17052143	1.00[EUR][1000 genomes]
rs28413740	1.00[EUR][1000 genomes]
rs28434358	1.00[EUR][1000 genomes]
rs28636773	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34540591	1.00[EUR][1000 genomes]
rs4687614	1.00[YRI][hapmap]
rs5743834	1.00[EUR][1000 genomes]
rs72947594	1.00[AMR][1000 genomes]
rs9813448	1.00[EUR][1000 genomes]
rs9813468	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9813489	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[EUR][1000 genomes]
rs9813653	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9814016	1.00[EUR][1000 genomes]
rs9815559	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9821916	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9824342	1.00[EUR][1000 genomes]
rs9828432	1.00[EUR][1000 genomes]
rs9828488	1.00[EUR][1000 genomes]
rs9831689	1.00[EUR][1000 genomes]
rs9834363	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9834919	0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9836166	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9843055	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9844178	0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9845752	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9864989	1.00[EUR][1000 genomes]
rs9868332	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 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	chr3:52395000-52443200	Weak transcription	Right Atrium	heart
2	chr3:52418600-52442200	Strong transcription	Fetal Intestine Small	intestine
3	chr3:52418800-52441800	Strong transcription	Brain Anterior Caudate	brain
4	chr3:52419000-52441800	Strong transcription	Liver	Liver
5	chr3:52419000-52442000	Strong transcription	Brain Hippocampus Middle	brain
6	chr3:52419000-52442600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:52419200-52441600	Strong transcription	Fetal Stomach	stomach
8	chr3:52419200-52441800	Strong transcription	Brain Angular Gyrus	brain
9	chr3:52419200-52442000	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr3:52420000-52442000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52420200-52442400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:52420200-52442600	Strong transcription	Fetal Intestine Large	intestine
14	chr3:52422600-52441800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:52425600-52442000	Strong transcription	Spleen	Spleen
16	chr3:52426600-52442200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:52430000-52442400	Strong transcription	Brain Substantia Nigra	brain
18	chr3:52430200-52442000	Strong transcription	Primary T cells from cord blood	blood
19	chr3:52430800-52442600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:52430800-52442600	Strong transcription	Brain Cingulate Gyrus	brain
21	chr3:52431000-52441600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:52431800-52440800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:52432000-52442400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:52432200-52440400	Strong transcription	Primary B cells from cord blood	blood
25	chr3:52432200-52442400	Strong transcription	Lung	lung
26	chr3:52432600-52439600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:52432600-52442200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:52432800-52441800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:52432800-52442000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:52432800-52442000	Strong transcription	Fetal Thymus	thymus
31	chr3:52432800-52442200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:52432800-52442400	Strong transcription	Thymus	Thymus
33	chr3:52432800-52442400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:52433000-52441600	Strong transcription	Fetal Brain Female	brain
35	chr3:52433000-52442400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:52433200-52442000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:52433200-52442000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:52433200-52442000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:52433200-52442600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:52433400-52439000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:52433400-52441200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:52433400-52442800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:52433600-52440600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:52433800-52442000	Strong transcription	Brain Germinal Matrix	brain
45	chr3:52433800-52442200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:52433800-52442400	Strong transcription	NHLF	lung
47	chr3:52434000-52442800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:52434200-52439800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr3:52434200-52440800	Strong transcription	Dnd41	blood
50	chr3:52434200-52441800	Strong transcription	Aorta	Aorta

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