Variant report

Variant	rs16996360
Chromosome Location	chr19:19902916-19902917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19885449..19887952-chr19:19901599..19903328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266904	Chromatin interaction
ENSG00000267419	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10404296	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10412885	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12710110	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975051	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs248930	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248931	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248932	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248933	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248934	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248936	0.94[CHB][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248937	0.81[EUR][1000 genomes]
rs248942	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248944	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248945	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248946	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248947	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248948	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248949	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248951	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248952	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248954	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087767	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762190	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808216	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808989	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4808991	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808995	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6511050	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246727	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248808	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256535	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106100	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109240	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111421	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv578799	chr19:19901136-19967970	ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16996360	ZNF506	Cis_1M	lymphoblastoid	RTeQTL
rs16996360	ZNF93	cis	cerebellum	SCAN
rs16996360	ZNF506	cis	normal skin	skin_eQTL
rs16996360	ATP13A1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
2	chr19:19888600-19904000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:19888600-19906400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr19:19888600-19906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:19888600-19909000	Weak transcription	K562	blood
6	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
7	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
8	chr19:19888800-19904000	Weak transcription	Hela-S3	cervix
9	chr19:19889600-19904600	Weak transcription	Colon Smooth Muscle	Colon
10	chr19:19894200-19904400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:19895400-19908200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:19895600-19903000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr19:19895600-19903200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:19895600-19903400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:19895600-19904200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:19895600-19907200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr19:19895600-19909000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
21	chr19:19895600-19909000	ZNF genes & repeats	Liver	Liver
22	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
24	chr19:19895800-19903000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr19:19895800-19903400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:19895800-19908200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:19895800-19914800	Strong transcription	Dnd41	blood
28	chr19:19896000-19903600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:19896000-19909200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:19896200-19903000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr19:19896400-19903200	Strong transcription	Fetal Brain Female	brain
32	chr19:19896400-19903400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:19896600-19905400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:19896600-19905800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:19896800-19908000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:19897000-19903000	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr19:19897000-19903200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:19897000-19904400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr19:19897000-19904400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:19897200-19903200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:19897200-19903400	Strong transcription	Brain Angular Gyrus	brain
42	chr19:19897200-19903400	Strong transcription	Fetal Muscle Leg	muscle
43	chr19:19897200-19903800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr19:19897200-19904000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr19:19897200-19904200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:19897200-19904600	Strong transcription	Osteobl	bone
47	chr19:19897200-19905800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr19:19897200-19906600	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:19897200-19907200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:19897200-19908600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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