Variant report

Variant	rs16964505
Chromosome Location	chr15:52048964-52048965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52047517..52051526-chr15:52055116..52057120,3	K562	blood:
2	chr15:52043733..52046292-chr15:52047210..52050045,3	MCF-7	breast:
3	chr15:52027911..52030761-chr15:52046678..52049036,2	K562	blood:
4	chr15:52043149..52046754-chr15:52046824..52050469,4	K562	blood:
5	chr15:51997400..52000250-chr15:52046573..52049240,2	MCF-7	breast:
6	chr15:52028579..52031295-chr15:52046217..52050933,5	MCF-7	breast:
7	chr15:52042908..52046919-chr15:52047131..52052382,6	MCF-7	breast:
8	chr15:52048901..52051193-chr15:52052461..52055031,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction
ENSG00000128872	Chromatin interaction
ENSG00000259377	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16953082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[EUR][1000 genomes]
rs16964486	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16964488	1.00[CEU][hapmap]
rs16964506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16964507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16964508	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16964510	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16964518	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16964528	0.88[EUR][1000 genomes]
rs16964532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.95[EUR][1000 genomes]
rs16964555	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16964561	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.90[EUR][1000 genomes]
rs16964579	0.90[EUR][1000 genomes]
rs16964585	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16964596	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.90[EUR][1000 genomes]
rs16964639	0.83[EUR][1000 genomes]
rs16964645	0.85[EUR][1000 genomes]
rs17705373	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1991267	1.00[JPT][hapmap]
rs2414115	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2570232	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[EUR][1000 genomes]
rs2593181	1.00[JPT][hapmap]
rs2623256	0.84[EUR][1000 genomes]
rs2899478	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3751595	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3794529	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4499184	0.82[ASN][1000 genomes]
rs4775971	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs56221158	0.97[EUR][1000 genomes]
rs7165299	1.00[LWK][hapmap]
rs7165594	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7166954	0.86[EUR][1000 genomes]
rs7167759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174616	1.00[CEU][hapmap]
rs7175121	1.00[CEU][hapmap]
rs7179971	0.86[EUR][1000 genomes]
rs7180093	0.86[EUR][1000 genomes]
rs73405364	0.80[EUR][1000 genomes]
rs7342575	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs74015757	0.91[EUR][1000 genomes]
rs74015761	0.91[EUR][1000 genomes]
rs8036648	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16964505	IL1B	trans	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52044400-52050800	Weak transcription	Gastric	stomach
2	chr15:52044600-52060000	Weak transcription	Esophagus	oesophagus
3	chr15:52044600-52060200	Weak transcription	Aorta	Aorta
4	chr15:52044800-52049800	Weak transcription	Psoas Muscle	Psoas
5	chr15:52044800-52050600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:52044800-52051000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:52044800-52051000	Weak transcription	Right Ventricle	heart
8	chr15:52044800-52060000	Weak transcription	Spleen	Spleen
9	chr15:52045000-52049800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:52045000-52049800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:52045000-52050600	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr15:52045000-52050800	Weak transcription	HMEC	breast
13	chr15:52045000-52060200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:52045200-52049800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:52045200-52050600	Weak transcription	Brain Germinal Matrix	brain
16	chr15:52045200-52053400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:52045400-52050400	Weak transcription	Fetal Brain Female	brain
18	chr15:52045400-52050600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:52045400-52050600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr15:52045400-52051000	Weak transcription	Left Ventricle	heart
21	chr15:52045600-52049800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:52045600-52050600	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:52045800-52049800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:52045800-52053200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:52046000-52050400	Weak transcription	Fetal Brain Male	brain
26	chr15:52046400-52049200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:52046800-52060000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:52047000-52049400	Enhancers	Primary B cells from cord blood	blood
29	chr15:52047000-52052400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:52047200-52053600	Enhancers	Brain Cingulate Gyrus	brain
31	chr15:52047400-52049200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:52047400-52049200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr15:52047400-52050800	Enhancers	Brain Anterior Caudate	brain
34	chr15:52047400-52050800	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr15:52047400-52050800	Enhancers	Brain Substantia Nigra	brain
36	chr15:52047400-52053600	Enhancers	Brain Hippocampus Middle	brain
37	chr15:52047600-52049000	Enhancers	Brain Angular Gyrus	brain
38	chr15:52048000-52049000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr15:52048000-52050800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:52048000-52050800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:52048000-52058000	Weak transcription	Primary T cells from cord blood	blood
42	chr15:52048200-52050600	Weak transcription	Fetal Intestine Small	intestine
43	chr15:52048200-52060000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:52048200-52060200	Weak transcription	Thymus	Thymus
45	chr15:52048400-52050800	Weak transcription	Lung	lung
46	chr15:52048600-52049000	Flanking Active TSS	K562	blood
47	chr15:52048600-52049200	Enhancers	Dnd41	blood
48	chr15:52048600-52052200	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr15:52048800-52049000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr15:52048800-52049000	Enhancers	Rectal Mucosa Donor 31	rectum

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