Variant report

Variant	rs16964513
Chromosome Location	chr15:52063179-52063180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52062590..52065272-chr15:52121050..52123108,2	MCF-7	breast:
2	chr15:52054450..52058295-chr15:52061213..52063877,3	MCF-7	breast:
3	chr15:52058591..52061806-chr15:52062033..52065705,3	K562	blood:

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10519324	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953079	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs16964509	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964517	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964530	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs16964531	1.00[YRI][hapmap]
rs17648915	0.90[AFR][1000 genomes]
rs17648927	0.90[AFR][1000 genomes]
rs17649601	1.00[EUR][1000 genomes]
rs17705437	0.90[AFR][1000 genomes]
rs2554357	1.00[EUR][1000 genomes]
rs57399438	0.90[AFR][1000 genomes]
rs58356723	1.00[EUR][1000 genomes]
rs58434025	0.90[AFR][1000 genomes]
rs58559761	0.90[AFR][1000 genomes]
rs58958163	1.00[EUR][1000 genomes]
rs59426894	0.90[AFR][1000 genomes]
rs59522140	1.00[EUR][1000 genomes]
rs60590663	0.90[AFR][1000 genomes]
rs73405314	0.90[AFR][1000 genomes]
rs73405317	0.90[AFR][1000 genomes]
rs73405321	0.90[AFR][1000 genomes]
rs73405322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73405324	0.90[AFR][1000 genomes]
rs73405338	0.90[AFR][1000 genomes]
rs73405339	0.90[AFR][1000 genomes]
rs73405346	0.90[AFR][1000 genomes]
rs73405351	0.90[AFR][1000 genomes]
rs73405368	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405370	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405377	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405389	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73405400	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407328	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407332	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73409029	1.00[EUR][1000 genomes]
rs73409034	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	esv3411789	chr15:52052789-52087519	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52051200-52077600	Weak transcription	Psoas Muscle	Psoas
2	chr15:52051400-52068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr15:52051400-52068400	Weak transcription	Stomach Mucosa	stomach
4	chr15:52052200-52064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:52052200-52068200	Weak transcription	Fetal Intestine Small	intestine
6	chr15:52052200-52068600	Weak transcription	HMEC	breast
7	chr15:52052200-52074600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:52052200-52076000	Weak transcription	Fetal Brain Male	brain
9	chr15:52052200-52101800	Weak transcription	Colonic Mucosa	Colon
10	chr15:52052400-52067000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:52052400-52068200	Weak transcription	Fetal Intestine Large	intestine
12	chr15:52052400-52073200	Weak transcription	NHDF-Ad	bronchial
13	chr15:52052400-52078400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:52052600-52065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:52052600-52106600	Weak transcription	HSMM	muscle
16	chr15:52053400-52090600	Weak transcription	Pancreas	Pancrea
17	chr15:52058400-52064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:52058400-52067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:52058600-52068200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:52058800-52072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:52060000-52063200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:52060000-52063600	Strong transcription	Ovary	ovary
23	chr15:52060200-52068200	Weak transcription	Liver	Liver
24	chr15:52060200-52103400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:52060400-52063600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:52060400-52064600	Strong transcription	Fetal Muscle Leg	muscle
27	chr15:52060400-52068400	Strong transcription	Thymus	Thymus
28	chr15:52060400-52069200	Weak transcription	Placenta	Placenta
29	chr15:52060400-52069800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr15:52060400-52079200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:52060400-52085400	Weak transcription	Fetal Lung	lung
32	chr15:52060600-52063200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:52060600-52063200	Weak transcription	K562	blood
34	chr15:52060600-52064000	Weak transcription	HUVEC	blood vessel
35	chr15:52060600-52064200	Weak transcription	Right Atrium	heart
36	chr15:52060600-52065200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:52060600-52065400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52060600-52065800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:52060600-52068600	Weak transcription	Brain Substantia Nigra	brain
40	chr15:52060600-52069000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:52060600-52073400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr15:52060600-52073600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:52060600-52087400	Weak transcription	Gastric	stomach
44	chr15:52060600-52088400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr15:52060600-52091000	Weak transcription	Right Ventricle	heart
46	chr15:52060800-52063400	Strong transcription	Brain Angular Gyrus	brain
47	chr15:52060800-52064600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:52060800-52067600	Strong transcription	Colon Smooth Muscle	Colon
49	chr15:52060800-52067800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr15:52060800-52068400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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