Variant report

Variant	rs16964645
Chromosome Location	chr15:52252625-52252626
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52241939..52245951-chr15:52252494..52254797,3	K562	blood:
2	chr15:52250643..52258110-chr15:52261122..52265819,12	MCF-7	breast:
3	chr15:52249529..52256191-chr15:52262317..52265170,10	MCF-7	breast:
4	chr15:52251464..52253860-chr15:52255270..52257201,2	K562	blood:

Variant related genes	Relation type
ENSG00000069956	Chromatin interaction
ENSG00000166477	Chromatin interaction

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

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

rs_ID	r²[population]
rs16953082	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964505	0.85[EUR][1000 genomes]
rs16964506	0.85[EUR][1000 genomes]
rs16964507	0.85[EUR][1000 genomes]
rs16964508	0.85[EUR][1000 genomes]
rs16964510	0.85[EUR][1000 genomes]
rs16964518	0.85[EUR][1000 genomes]
rs16964528	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16964532	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964555	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964561	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964579	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964585	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964596	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964639	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991267	0.90[ASN][1000 genomes]
rs2258248	0.90[ASN][1000 genomes]
rs2570265	0.90[ASN][1000 genomes]
rs2593181	0.90[ASN][1000 genomes]
rs2593184	0.90[ASN][1000 genomes]
rs2623291	0.90[ASN][1000 genomes]
rs2959296	0.90[ASN][1000 genomes]
rs56221158	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52179600-52259800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52200400-52262200	Weak transcription	Stomach Mucosa	stomach
3	chr15:52222600-52259800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:52226000-52255200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:52226200-52254800	Strong transcription	Thymus	Thymus
6	chr15:52226200-52255000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:52226200-52259400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52227400-52255000	Strong transcription	Liver	Liver
9	chr15:52227400-52258400	Strong transcription	Dnd41	blood
10	chr15:52227800-52255000	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr15:52229800-52254200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:52232800-52256000	Strong transcription	Fetal Muscle Leg	muscle
13	chr15:52233000-52258000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr15:52233200-52255200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:52233200-52255200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:52233600-52258000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:52235600-52255000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr15:52235600-52255200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:52235600-52256000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:52235600-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:52235800-52255000	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr15:52235800-52255000	Strong transcription	A549	lung
23	chr15:52235800-52255000	Strong transcription	Osteobl	bone
24	chr15:52235800-52255200	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:52235800-52255200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:52235800-52256000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:52235800-52258000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:52235800-52258600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr15:52235800-52259200	Strong transcription	Hela-S3	cervix
30	chr15:52236000-52255000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr15:52236000-52255200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:52236000-52255200	Strong transcription	Fetal Lung	lung
33	chr15:52236000-52255600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:52236000-52256200	Strong transcription	HepG2	liver
35	chr15:52236000-52258000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:52236000-52258600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:52236000-52258800	Strong transcription	Fetal Thymus	thymus
38	chr15:52236200-52255600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:52236200-52258800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:52236400-52254800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:52236600-52255200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:52236800-52254600	Strong transcription	Fetal Intestine Large	intestine
43	chr15:52236800-52255000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:52237000-52255200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52237000-52255600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:52237000-52256000	Strong transcription	Fetal Stomach	stomach
47	chr15:52237000-52258400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:52237200-52255200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:52237200-52257600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:52237400-52254000	Strong transcription	Brain Anterior Caudate	brain

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