Variant report

Variant	rs16964750
Chromosome Location	chr15:52463924-52463925
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52462256..52465166-chr15:52466100..52468864,2	MCF-7	breast:
2	chr15:52463801..52465460-chr21:45777828..45779686,2	MCF-7	breast:
3	chr15:52462679..52469948-chr15:52470344..52473249,9	MCF-7	breast:
4	chr15:52463285..52465150-chr15:52473016..52475731,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs12916135	0.86[AFR][1000 genomes]
rs16953085	1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	1.00[EUR][1000 genomes]
rs28656256	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663157	1.00[EUR][1000 genomes]
rs35712143	0.86[AFR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs4776010	0.83[AFR][1000 genomes]
rs4776013	0.83[AFR][1000 genomes]
rs59195841	1.00[EUR][1000 genomes]
rs59289747	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60397096	1.00[EUR][1000 genomes]
rs66566761	0.86[AFR][1000 genomes]
rs67163040	0.83[AFR][1000 genomes]
rs67725996	0.85[AFR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167133	1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs7183278	0.83[AFR][1000 genomes]
rs730945	1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs73404813	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8023921	1.00[EUR][1000 genomes]
rs8024311	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8025737	0.82[AFR][1000 genomes]
rs8035146	1.00[EUR][1000 genomes]
rs8040458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52429800-52470200	Weak transcription	Fetal Brain Male	brain
2	chr15:52442200-52470400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:52442200-52471000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:52442200-52471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:52442600-52470000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:52442600-52470400	Weak transcription	HMEC	breast
7	chr15:52443000-52470800	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:52445600-52471000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:52447400-52471000	Weak transcription	Right Atrium	heart
10	chr15:52448800-52465200	Weak transcription	Liver	Liver
11	chr15:52454200-52464000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:52454200-52468200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:52455600-52470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:52455800-52467800	Weak transcription	Thymus	Thymus
15	chr15:52455800-52468400	Weak transcription	Hela-S3	cervix
16	chr15:52455800-52471000	Weak transcription	Aorta	Aorta
17	chr15:52455800-52471000	Weak transcription	Gastric	stomach
18	chr15:52456000-52464800	Weak transcription	Pancreas	Pancrea
19	chr15:52456000-52468400	Weak transcription	Ovary	ovary
20	chr15:52456000-52470000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:52456000-52470600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:52456000-52470600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:52456000-52471000	Weak transcription	HSMMtube	muscle
24	chr15:52456200-52467200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:52456200-52468200	Weak transcription	Fetal Brain Female	brain
26	chr15:52456200-52468400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:52456200-52470200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:52456200-52470800	Weak transcription	Fetal Stomach	stomach
29	chr15:52456200-52470800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:52456200-52471000	Weak transcription	Spleen	Spleen
31	chr15:52462200-52464400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr15:52462600-52464400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr15:52462600-52464400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr15:52462600-52464400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr15:52462800-52464400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr15:52463000-52464000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr15:52463000-52464000	Enhancers	Fetal Thymus	thymus
38	chr15:52463000-52464200	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:52463000-52464200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr15:52463000-52464400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52463200-52464000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:52463200-52464400	Enhancers	Primary T cells from cord blood	blood
43	chr15:52463200-52464400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:52463200-52464800	Enhancers	Primary B cells from peripheral blood	blood
45	chr15:52463200-52470600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:52463400-52464000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr15:52463400-52464000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:52463400-52464200	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr15:52463400-52464200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr15:52463400-52464400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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