Variant report

Variant	rs6511050
Chromosome Location	chr19:19909720-19909721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10404296	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10412885	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12710110	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs16996360	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]
rs248930	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248931	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248932	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248933	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248934	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248936	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs248942	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248948	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248949	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248951	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248952	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248954	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762190	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808216	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808989	0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4808991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808995	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808998	0.88[AFR][1000 genomes]
rs7246727	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256535	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106100	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8109240	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111421	0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
11	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6511050	ZNF506	cis	normal skin	skin_eQTL
rs6511050	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
2	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
3	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
4	chr19:19895000-19931200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:19895400-19914800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:19895400-19914800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:19895600-19914800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:19895600-19915000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:19895800-19914800	Strong transcription	Dnd41	blood
10	chr19:19897200-19918600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr19:19900000-19915200	Weak transcription	HepG2	liver
12	chr19:19902000-19914400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:19902600-19922400	Weak transcription	Right Ventricle	heart
14	chr19:19902600-19931600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:19902800-19910200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:19903200-19916400	Weak transcription	Fetal Brain Male	brain
17	chr19:19903800-19911000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:19903800-19911000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr19:19905000-19930000	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:19905600-19913600	Weak transcription	Brain Substantia Nigra	brain
21	chr19:19905800-19910400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:19906200-19914000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr19:19906400-19920400	Weak transcription	Brain Angular Gyrus	brain
24	chr19:19906400-19923200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:19906800-19910400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:19906800-19916200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:19907000-19909800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:19907000-19910000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:19907000-19911400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr19:19907000-19911600	Weak transcription	Gastric	stomach
31	chr19:19907000-19913600	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:19907000-19913800	Weak transcription	Placenta	Placenta
33	chr19:19907000-19914000	Weak transcription	Spleen	Spleen
34	chr19:19907000-19914400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:19907000-19916200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr19:19907000-19916400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr19:19907000-19923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:19907000-19931400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr19:19907000-19931600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:19907200-19911600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr19:19907200-19912800	Weak transcription	Brain Anterior Caudate	brain
42	chr19:19907200-19913400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:19907200-19913600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:19907200-19913600	Weak transcription	Adipose Nuclei	Adipose
45	chr19:19907200-19913600	Weak transcription	HSMMtube	muscle
46	chr19:19907200-19913800	Weak transcription	Ovary	ovary
47	chr19:19907200-19914200	Weak transcription	Pancreas	Pancrea
48	chr19:19907200-19915800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:19907600-19911400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:19907600-19929600	Weak transcription	Small Intestine	intestine

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