Variant report

Variant	rs248930
Chromosome Location	chr19:19896115-19896116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10404296	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10412885	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12710110	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975051	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16996360	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248931	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248932	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248933	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248934	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248936	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248937	0.81[EUR][1000 genomes]
rs248942	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248948	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248949	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248951	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248954	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762190	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808216	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4808989	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808995	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246727	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256535	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106100	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8109240	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111421	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs248930	LINC00663	cis	Artery Tibial	GTEx
rs248930	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19888000-19897000	Weak transcription	Left Ventricle	heart
2	chr19:19888000-19897200	Weak transcription	Aorta	Aorta
3	chr19:19888000-19899600	Weak transcription	Ovary	ovary
4	chr19:19888200-19902200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:19888400-19897200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:19888400-19897200	Weak transcription	Brain Angular Gyrus	brain
7	chr19:19888400-19897200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:19888400-19897200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:19888400-19897400	Weak transcription	Placenta	Placenta
10	chr19:19888400-19899000	Weak transcription	Right Ventricle	heart
11	chr19:19888400-19899400	Weak transcription	HSMM	muscle
12	chr19:19888400-19927800	Weak transcription	Psoas Muscle	Psoas
13	chr19:19888600-19896200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:19888600-19896200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:19888600-19896400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr19:19888600-19896400	Weak transcription	Fetal Thymus	thymus
17	chr19:19888600-19896600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:19888600-19896600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:19888600-19897000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:19888600-19897000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:19888600-19897200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:19888600-19897200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:19888600-19897200	Weak transcription	Fetal Lung	lung
24	chr19:19888600-19897200	Weak transcription	Osteobl	bone
25	chr19:19888600-19897400	Weak transcription	HSMMtube	muscle
26	chr19:19888600-19897800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:19888600-19898600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:19888600-19899200	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:19888600-19899400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:19888600-19899600	Weak transcription	Brain Germinal Matrix	brain
31	chr19:19888600-19899600	Weak transcription	Colonic Mucosa	Colon
32	chr19:19888600-19901000	Weak transcription	HMEC	breast
33	chr19:19888600-19901800	Weak transcription	Small Intestine	intestine
34	chr19:19888600-19902000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:19888600-19904000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:19888600-19906400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:19888600-19906800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr19:19888600-19909000	Weak transcription	K562	blood
39	chr19:19888600-19911000	Weak transcription	HUVEC	blood vessel
40	chr19:19888600-19931800	Weak transcription	Fetal Heart	heart
41	chr19:19888800-19897000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:19888800-19897000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:19888800-19897000	Weak transcription	Spleen	Spleen
44	chr19:19888800-19897200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:19888800-19897200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:19888800-19897200	Weak transcription	Fetal Muscle Leg	muscle
47	chr19:19888800-19897200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:19888800-19897200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:19888800-19897400	Weak transcription	Adipose Nuclei	Adipose
50	chr19:19888800-19897800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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